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| 2020-03-01 21:45:17,828 mriqc:IMPORTANT | |
| Running MRIQC version 0.15.0: | |
| * BIDS dataset path: /data. | |
| * Output folder: /out. | |
| * Analysis levels: group, participant. | |
| 2020-03-01 21:45:22,119 py.warnings:WARNING /usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__ | |
| return f(*args, **kwds) | |
| 2020-03-01 21:45:22,694 py.warnings:WARNING /usr/local/miniconda/lib/python3.7/site-packages/sklearn/metrics/classification.py:349: DeprecationWarning: invalid escape sequence \k | |
| """ | |
| 2020-03-01 21:45:22,698 py.warnings:WARNING /usr/local/miniconda/lib/python3.7/site-packages/sklearn/metrics/cluster/supervised.py:578: DeprecationWarning: invalid escape sequence \s | |
| """ | |
| 2020-03-01 21:45:23,737 py.warnings:WARNING /usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__ | |
| return f(*args, **kwds) | |
| 2020-03-01 21:45:24,935 py.warnings:WARNING /usr/local/miniconda/lib/python3.7/site-packages/jedi/evaluate/arguments.py:95: DeprecationWarning: invalid escape sequence \[ | |
| match = re.match('(?:(?:(\[),? ?|, ?|)(\w+)|, ?/)\]*', string) | |
| 2020-03-01 21:45:26,025 py.warnings:WARNING /usr/local/miniconda/lib/python3.7/site-packages/ipywidgets/widgets/trait_types.py:148: DeprecationWarning: invalid escape sequence \- | |
| _number_format_re = re.compile('^(?:(.)?([<>=^]))?([+\-\( ])?([$#])?(0)?(\d+)?(,)?(\.\d+)?([a-z%])?$', re.I) | |
| 2020-03-01 21:45:26,116 py.warnings:WARNING /usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__ | |
| return f(*args, **kwds) | |
| 2020-03-01 21:45:26,128 py.warnings:WARNING /usr/local/miniconda/lib/python3.7/site-packages/sklearn/datasets/samples_generator.py:839: DeprecationWarning: invalid escape sequence \# | |
| """ | |
| 2020-03-01 21:45:26,129 py.warnings:WARNING /usr/local/miniconda/lib/python3.7/site-packages/sklearn/datasets/samples_generator.py:1429: DeprecationWarning: invalid escape sequence \c | |
| """ | |
| 2020-03-01 21:45:26,161 py.warnings:WARNING /usr/local/miniconda/lib/python3.7/site-packages/nilearn/datasets/neurovault.py:16: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working | |
| from collections import Container | |
| 2020-03-01 21:45:26,216 py.warnings:WARNING /usr/local/miniconda/lib/python3.7/site-packages/sklearn/decomposition/nmf.py:972: DeprecationWarning: invalid escape sequence \s | |
| """ | |
| 2020-03-01 21:45:26,287 py.warnings:WARNING /usr/local/miniconda/lib/python3.7/site-packages/sklearn/linear_model/omp.py:343: DeprecationWarning: invalid escape sequence \g | |
| """ | |
| 2020-03-01 21:45:26,449 py.warnings:WARNING /usr/local/miniconda/lib/python3.7/site-packages/svgutils/compose.py:347: DeprecationWarning: invalid escape sequence \. | |
| m = re.match('([0-9]+\.?[0-9]*)([a-z]+)', measure) | |
| 2020-03-01 21:45:26,599 py.warnings:WARNING /usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/afni/utils.py:214: DeprecationWarning: invalid escape sequence \d | |
| pattern = 'x=(?P<x_min>-?\d+)\.\.(?P<x_max>-?\d+) '\ | |
| 2020-03-01 21:45:26,899 py.warnings:WARNING /usr/local/miniconda/lib/python3.7/site-packages/networkx/classes/reportviews.py:95: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working | |
| from collections import Mapping, Set, Iterable | |
| 2020-03-01 21:45:26,941 py.warnings:WARNING /usr/local/miniconda/lib/python3.7/site-packages/networkx/generators/geometric.py:275: DeprecationWarning: invalid escape sequence \l | |
| """ | |
| 2020-03-01 21:45:26,976 py.warnings:WARNING /usr/local/miniconda/lib/python3.7/site-packages/networkx/algorithms/cluster.py:537: DeprecationWarning: invalid escape sequence \m | |
| """ | |
| 2020-03-01 21:45:27,054 py.warnings:WARNING /usr/local/miniconda/lib/python3.7/site-packages/networkx/algorithms/reciprocity.py:47: DeprecationWarning: invalid escape sequence \i | |
| """ | |
| 2020-03-01 21:45:27,062 py.warnings:WARNING /usr/local/miniconda/lib/python3.7/site-packages/networkx/algorithms/shortest_paths/weighted.py:1996: DeprecationWarning: invalid escape sequence \p | |
| """ | |
| 2020-03-01 21:45:27,182 py.warnings:WARNING /usr/local/miniconda/lib/python3.7/site-packages/networkx/generators/line.py:113: DeprecationWarning: invalid escape sequence \{ | |
| """ | |
| 2020-03-01 21:45:27,248 py.warnings:WARNING /usr/local/miniconda/lib/python3.7/site-packages/networkx/linalg/modularitymatrix.py:74: DeprecationWarning: invalid escape sequence \o | |
| """ | |
| 200301-21:45:28,17 nipype.workflow INFO: | |
| Building anatomical MRIQC workflow, datasets list: ['sub-01/ses-01/anat/sub-01_ses-01_T1w.nii.gz'] | |
| 2020-03-01 21:45:28,017 nipype.workflow:INFO Building anatomical MRIQC workflow, datasets list: ['sub-01/ses-01/anat/sub-01_ses-01_T1w.nii.gz'] | |
| 200301-21:45:28,210 nipype.workflow INFO: | |
| Building anatomical MRIQC workflow, datasets list: ['sub-01/ses-01/anat/sub-01_ses-01_T2w.nii.gz'] | |
| 2020-03-01 21:45:28,210 nipype.workflow:INFO Building anatomical MRIQC workflow, datasets list: ['sub-01/ses-01/anat/sub-01_ses-01_T2w.nii.gz'] | |
| 2020-03-01 21:45:36,988 py.warnings:WARNING /usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__ | |
| return f(*args, **kwds) | |
| 2020-03-01 21:45:37,024 py.warnings:WARNING /usr/local/miniconda/lib/python3.7/site-packages/sklearn/metrics/classification.py:349: DeprecationWarning: invalid escape sequence \k | |
| """ | |
| 2020-03-01 21:45:37,027 py.warnings:WARNING /usr/local/miniconda/lib/python3.7/site-packages/sklearn/metrics/cluster/supervised.py:578: DeprecationWarning: invalid escape sequence \s | |
| """ | |
| 2020-03-01 21:45:37,107 py.warnings:WARNING /usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/fsl/utils.py:854: DeprecationWarning: invalid escape sequence \ | |
| 'Rotation\ &\ Translation\ Matrix:\n(?P<rot_tran_mat>[0-9\.\ \n-]+)[\s\n]*' | |
| 2020-03-01 21:45:37,107 py.warnings:WARNING /usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/fsl/utils.py:863: DeprecationWarning: invalid escape sequence \. | |
| '(?P<fwd_half_xfm>[0-9\.\ \n-]+)[\s\n]*' | |
| 2020-03-01 21:45:37,248 py.warnings:WARNING /usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__ | |
| return f(*args, **kwds) | |
| 2020-03-01 21:45:37,258 py.warnings:WARNING /usr/local/miniconda/lib/python3.7/site-packages/sklearn/datasets/samples_generator.py:839: DeprecationWarning: invalid escape sequence \# | |
| """ | |
| 2020-03-01 21:45:37,258 py.warnings:WARNING /usr/local/miniconda/lib/python3.7/site-packages/sklearn/datasets/samples_generator.py:1429: DeprecationWarning: invalid escape sequence \c | |
| """ | |
| 2020-03-01 21:45:37,283 py.warnings:WARNING /usr/local/miniconda/lib/python3.7/site-packages/nilearn/datasets/neurovault.py:16: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working | |
| from collections import Container | |
| 2020-03-01 21:45:37,322 py.warnings:WARNING /usr/local/miniconda/lib/python3.7/site-packages/sklearn/decomposition/nmf.py:972: DeprecationWarning: invalid escape sequence \s | |
| """ | |
| 2020-03-01 21:45:37,368 py.warnings:WARNING /usr/local/miniconda/lib/python3.7/site-packages/sklearn/linear_model/omp.py:343: DeprecationWarning: invalid escape sequence \g | |
| """ | |
| 2020-03-01 21:45:37,561 py.warnings:WARNING /usr/local/miniconda/lib/python3.7/site-packages/grabbit/core.py:780: DeprecationWarning: invalid escape sequence \{ | |
| to_rep = re.findall('\{(.*?)\}', template) | |
| 2020-03-01 21:45:37,561 py.warnings:WARNING /usr/local/miniconda/lib/python3.7/site-packages/grabbit/core.py:784: DeprecationWarning: invalid escape sequence \% | |
| template += '[^\%s]*$' % os.path.sep | |
| 2020-03-01 21:45:37,573 py.warnings:WARNING /usr/local/miniconda/lib/python3.7/site-packages/grabbit/external/inflect.py:845: DeprecationWarning: invalid escape sequence \S | |
| 'general': ['(?!major|lieutenant|brigadier|adjutant|.*star)\S+'], | |
| 2020-03-01 21:45:37,581 py.warnings:WARNING /usr/local/miniconda/lib/python3.7/site-packages/grabbit/extensions/writable.py:33: DeprecationWarning: invalid escape sequence \| | |
| match = re.search('([^|<]+)(<.*?>)?(\|.*)?', ent) | |
| 2020-03-01 21:45:37,581 py.warnings:WARNING /usr/local/miniconda/lib/python3.7/site-packages/grabbit/extensions/writable.py:92: DeprecationWarning: invalid escape sequence \[ | |
| optional_patterns = re.findall('\[(.*?)\]', pattern) | |
| 2020-03-01 21:45:37,706 mriqc:WARNING Anonymized quality metrics (IQMs) will be submitted to MRIQC's metrics repository. Submission of IQMs can be disabled using the ``--no-sub`` argument. Please visit https://mriqc.readthedocs.io/en/latest/dsa.html to revise MRIQC's Data Sharing Agreement. | |
| 2020-03-01 21:45:38,278 py.warnings:WARNING /usr/local/miniconda/lib/python3.7/site-packages/numpy/matrixlib/defmatrix.py:68: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. | |
| return matrix(data, dtype=dtype, copy=False) | |
| 2020-03-01 21:45:40,278 py.warnings:WARNING /usr/local/miniconda/lib/python3.7/site-packages/numpy/matrixlib/defmatrix.py:68: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. | |
| return matrix(data, dtype=dtype, copy=False) | |
| 200301-21:45:42,391 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.funcMRIQC.non_steady_state_detector" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/funcMRIQC/_in_file_..data..sub-01..ses-01..func..sub-01_ses-01_task-Stroop_run-01_bold.nii.gz/non_steady_state_detector". | |
| 200301-21:45:42,404 nipype.workflow INFO: | |
| [Node] Running "non_steady_state_detector" ("nipype.algorithms.confounds.NonSteadyStateDetector") | |
| 200301-21:45:44,392 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.conform" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT1w/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/conform". | |
| 2020-03-01 21:45:44,392 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.conform" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT1w/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/conform". | |
| 200301-21:45:44,405 nipype.workflow INFO: | |
| [Node] Running "conform" ("mriqc.interfaces.common.ConformImage") | |
| 2020-03-01 21:45:44,405 nipype.workflow:INFO [Node] Running "conform" ("mriqc.interfaces.common.ConformImage") | |
| 200301-21:45:47,21 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT1w.conform". | |
| 2020-03-01 21:45:47,021 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT1w.conform". | |
| 200301-21:45:47,675 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.funcMRIQC.non_steady_state_detector". | |
| 200301-21:45:49,28 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.ComputeIQMs.metadata" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT1w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/metadata". | |
| 200301-21:45:49,41 nipype.workflow INFO: | |
| [Node] Running "metadata" ("niworkflows.interfaces.bids.ReadSidecarJSON") | |
| 200301-21:45:49,116 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT1w.ComputeIQMs.metadata". | |
| 200301-21:45:49,616 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.funcMRIQC.sanitize" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/funcMRIQC/_in_file_..data..sub-01..ses-01..func..sub-01_ses-01_task-Stroop_run-01_bold.nii.gz/sanitize". | |
| 2020-03-01 21:45:49,616 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.funcMRIQC.sanitize" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/funcMRIQC/_in_file_..data..sub-01..ses-01..func..sub-01_ses-01_task-Stroop_run-01_bold.nii.gz/sanitize". | |
| 200301-21:45:49,618 nipype.workflow INFO: | |
| [Node] Running "sanitize" ("niworkflows.interfaces.utils.SanitizeImage") | |
| 2020-03-01 21:45:49,618 nipype.workflow:INFO [Node] Running "sanitize" ("niworkflows.interfaces.utils.SanitizeImage") | |
| 200301-21:45:50,172 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.ReportsWorkflow.PlotMosaicNoise" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT1w/ReportsWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/PlotMosaicNoise". | |
| 2020-03-01 21:45:50,172 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.ReportsWorkflow.PlotMosaicNoise" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT1w/ReportsWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/PlotMosaicNoise". | |
| 200301-21:45:50,175 nipype.workflow INFO: | |
| [Node] Running "PlotMosaicNoise" ("mriqc.interfaces.viz.PlotMosaic") | |
| 2020-03-01 21:45:50,175 nipype.workflow:INFO [Node] Running "PlotMosaicNoise" ("mriqc.interfaces.viz.PlotMosaic") | |
| 200301-21:45:50,506 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.AirMaskWorkflow.RotationMask" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT1w/AirMaskWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/RotationMask". | |
| 2020-03-01 21:45:50,506 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.AirMaskWorkflow.RotationMask" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT1w/AirMaskWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/RotationMask". | |
| 200301-21:45:50,515 nipype.workflow INFO: | |
| [Node] Running "RotationMask" ("mriqc.interfaces.anatomical.RotationMask") | |
| 2020-03-01 21:45:50,515 nipype.workflow:INFO [Node] Running "RotationMask" ("mriqc.interfaces.anatomical.RotationMask") | |
| 200301-21:45:52,845 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT1w.AirMaskWorkflow.RotationMask". | |
| 2020-03-01 21:45:52,845 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT1w.AirMaskWorkflow.RotationMask". | |
| 200301-21:45:54,383 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.AFNISkullStripWorkflow.inu_n4" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT1w/AFNISkullStripWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/inu_n4". | |
| 2020-03-01 21:45:54,383 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.AFNISkullStripWorkflow.inu_n4" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT1w/AFNISkullStripWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/inu_n4". | |
| 200301-21:45:54,386 nipype.workflow INFO: | |
| [Node] Running "inu_n4" ("nipype.interfaces.ants.segmentation.N4BiasFieldCorrection"), a CommandLine Interface with command: | |
| N4BiasFieldCorrection -d 3 --input-image /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT1w/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/conform/sub-01_ses-01_T1w_conformed.nii.gz --output [ sub-01_ses-01_T1w_conformed_corrected.nii.gz, sub-01_ses-01_T1w_conformed_bias.nii.gz ] | |
| 2020-03-01 21:45:54,386 nipype.workflow:INFO [Node] Running "inu_n4" ("nipype.interfaces.ants.segmentation.N4BiasFieldCorrection"), a CommandLine Interface with command: | |
| N4BiasFieldCorrection -d 3 --input-image /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT1w/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/conform/sub-01_ses-01_T1w_conformed.nii.gz --output [ sub-01_ses-01_T1w_conformed_corrected.nii.gz, sub-01_ses-01_T1w_conformed_bias.nii.gz ] | |
| 200301-21:46:09,538 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT1w.ReportsWorkflow.PlotMosaicNoise". | |
| 2020-03-01 21:46:09,538 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT1w.ReportsWorkflow.PlotMosaicNoise". | |
| 200301-21:46:10,432 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.conform" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT2w/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/conform". | |
| 2020-03-01 21:46:10,432 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.conform" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT2w/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/conform". | |
| 200301-21:46:10,435 nipype.workflow INFO: | |
| [Node] Running "conform" ("mriqc.interfaces.common.ConformImage") | |
| 2020-03-01 21:46:10,435 nipype.workflow:INFO [Node] Running "conform" ("mriqc.interfaces.common.ConformImage") | |
| 200301-21:46:12,630 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT2w.conform". | |
| 2020-03-01 21:46:12,630 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT2w.conform". | |
| 200301-21:46:14,431 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.ReportsWorkflow.PlotMosaicNoise" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT2w/ReportsWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/PlotMosaicNoise". | |
| 2020-03-01 21:46:14,431 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.ReportsWorkflow.PlotMosaicNoise" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT2w/ReportsWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/PlotMosaicNoise". | |
| 200301-21:46:14,435 nipype.workflow INFO: | |
| [Node] Running "PlotMosaicNoise" ("mriqc.interfaces.viz.PlotMosaic") | |
| 2020-03-01 21:46:14,435 nipype.workflow:INFO [Node] Running "PlotMosaicNoise" ("mriqc.interfaces.viz.PlotMosaic") | |
| 200301-21:46:19,282 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.funcMRIQC.sanitize". | |
| 2020-03-01 21:46:19,282 nipype.workflow:INFO [Node] Finished "workflow_enumerator.funcMRIQC.sanitize". | |
| 200301-21:46:20,441 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.funcMRIQC.ReportsWorkflow.SpikesMask" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/funcMRIQC/ReportsWorkflow/_in_file_..data..sub-01..ses-01..func..sub-01_ses-01_task-Stroop_run-01_bold.nii.gz/SpikesMask". | |
| 2020-03-01 21:46:20,441 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.funcMRIQC.ReportsWorkflow.SpikesMask" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/funcMRIQC/ReportsWorkflow/_in_file_..data..sub-01..ses-01..func..sub-01_ses-01_task-Stroop_run-01_bold.nii.gz/SpikesMask". | |
| 200301-21:46:20,444 nipype.workflow INFO: | |
| [Node] Running "SpikesMask" ("nipype.interfaces.utility.wrappers.Function") | |
| 2020-03-01 21:46:20,444 nipype.workflow:INFO [Node] Running "SpikesMask" ("nipype.interfaces.utility.wrappers.Function") | |
| 200301-21:46:31,694 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.funcMRIQC.ReportsWorkflow.SpikesMask". | |
| 2020-03-01 21:46:31,694 nipype.workflow:INFO [Node] Finished "workflow_enumerator.funcMRIQC.ReportsWorkflow.SpikesMask". | |
| 200301-21:46:32,450 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.funcMRIQC.ReportsWorkflow.SpikesFinderBgMask" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/funcMRIQC/ReportsWorkflow/_in_file_..data..sub-01..ses-01..func..sub-01_ses-01_task-Stroop_run-01_bold.nii.gz/SpikesFinderBgMask". | |
| 2020-03-01 21:46:32,450 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.funcMRIQC.ReportsWorkflow.SpikesFinderBgMask" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/funcMRIQC/ReportsWorkflow/_in_file_..data..sub-01..ses-01..func..sub-01_ses-01_task-Stroop_run-01_bold.nii.gz/SpikesFinderBgMask". | |
| 200301-21:46:32,452 nipype.workflow INFO: | |
| [Node] Running "SpikesFinderBgMask" ("mriqc.interfaces.functional.Spikes") | |
| 2020-03-01 21:46:32,452 nipype.workflow:INFO [Node] Running "SpikesFinderBgMask" ("mriqc.interfaces.functional.Spikes") | |
| 200301-21:46:36,571 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT2w.ReportsWorkflow.PlotMosaicNoise". | |
| 2020-03-01 21:46:36,571 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT2w.ReportsWorkflow.PlotMosaicNoise". | |
| 200301-21:46:40,495 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.funcMRIQC.fMRI_HMC_afni.gen_ref" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/funcMRIQC/fMRI_HMC_afni/_in_file_..data..sub-01..ses-01..func..sub-01_ses-01_task-Stroop_run-01_bold.nii.gz/gen_ref". | |
| 2020-03-01 21:46:40,495 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.funcMRIQC.fMRI_HMC_afni.gen_ref" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/funcMRIQC/fMRI_HMC_afni/_in_file_..data..sub-01..ses-01..func..sub-01_ses-01_task-Stroop_run-01_bold.nii.gz/gen_ref". | |
| 200301-21:46:40,509 nipype.workflow INFO: | |
| [Node] Running "gen_ref" ("niworkflows.interfaces.registration.EstimateReferenceImage") | |
| 2020-03-01 21:46:40,509 nipype.workflow:INFO [Node] Running "gen_ref" ("niworkflows.interfaces.registration.EstimateReferenceImage") | |
| 200301-21:46:43,394 nipype.interface INFO: | |
| stderr 2020-03-01T21:46:43.394263:++ 3dvolreg: AFNI version=AFNI_17.3.03 (Nov 9 2017) [64-bit] | |
| 2020-03-01 21:46:43,394 nipype.interface:INFO stderr 2020-03-01T21:46:43.394263:++ 3dvolreg: AFNI version=AFNI_17.3.03 (Nov 9 2017) [64-bit] | |
| 200301-21:46:43,394 nipype.interface INFO: | |
| stderr 2020-03-01T21:46:43.394263:++ Authored by: RW Cox | |
| 2020-03-01 21:46:43,394 nipype.interface:INFO stderr 2020-03-01T21:46:43.394263:++ Authored by: RW Cox | |
| 200301-21:46:43,420 nipype.interface INFO: | |
| stderr 2020-03-01T21:46:43.419977:[7m*+ WARNING:[0m If you are performing spatial transformations on an oblique dset, | |
| 2020-03-01 21:46:43,420 nipype.interface:INFO stderr 2020-03-01T21:46:43.419977:[7m*+ WARNING:[0m If you are performing spatial transformations on an oblique dset, | |
| 200301-21:46:43,420 nipype.interface INFO: | |
| stderr 2020-03-01T21:46:43.419977: such as /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/funcMRIQC/fMRI_HMC_afni/_in_file_..data..sub-01..ses-01..func..sub-01_ses-01_task-Stroop_run-01_bold.nii.gz/gen_ref/slice.nii.gz, | |
| 2020-03-01 21:46:43,420 nipype.interface:INFO stderr 2020-03-01T21:46:43.419977: such as /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/funcMRIQC/fMRI_HMC_afni/_in_file_..data..sub-01..ses-01..func..sub-01_ses-01_task-Stroop_run-01_bold.nii.gz/gen_ref/slice.nii.gz, | |
| 200301-21:46:43,420 nipype.interface INFO: | |
| stderr 2020-03-01T21:46:43.419977: or viewing/combining it with volumes of differing obliquity, | |
| 2020-03-01 21:46:43,420 nipype.interface:INFO stderr 2020-03-01T21:46:43.419977: or viewing/combining it with volumes of differing obliquity, | |
| 200301-21:46:43,420 nipype.interface INFO: | |
| stderr 2020-03-01T21:46:43.419977: you should consider running: | |
| 2020-03-01 21:46:43,420 nipype.interface:INFO stderr 2020-03-01T21:46:43.419977: you should consider running: | |
| 200301-21:46:43,420 nipype.interface INFO: | |
| stderr 2020-03-01T21:46:43.419977: 3dWarp -deoblique | |
| 2020-03-01 21:46:43,420 nipype.interface:INFO stderr 2020-03-01T21:46:43.419977: 3dWarp -deoblique | |
| 200301-21:46:43,420 nipype.interface INFO: | |
| stderr 2020-03-01T21:46:43.419977: on this and other oblique datasets in the same session. | |
| 2020-03-01 21:46:43,420 nipype.interface:INFO stderr 2020-03-01T21:46:43.419977: on this and other oblique datasets in the same session. | |
| 200301-21:46:43,420 nipype.interface INFO: | |
| stderr 2020-03-01T21:46:43.419977: See 3dWarp -help for details. | |
| 2020-03-01 21:46:43,420 nipype.interface:INFO stderr 2020-03-01T21:46:43.419977: See 3dWarp -help for details. | |
| 200301-21:46:43,420 nipype.interface INFO: | |
| stderr 2020-03-01T21:46:43.419977:++ Oblique dataset:/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/funcMRIQC/fMRI_HMC_afni/_in_file_..data..sub-01..ses-01..func..sub-01_ses-01_task-Stroop_run-01_bold.nii.gz/gen_ref/slice.nii.gz is 20.932278 degrees from plumb. | |
| 2020-03-01 21:46:43,420 nipype.interface:INFO stderr 2020-03-01T21:46:43.419977:++ Oblique dataset:/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/funcMRIQC/fMRI_HMC_afni/_in_file_..data..sub-01..ses-01..func..sub-01_ses-01_task-Stroop_run-01_bold.nii.gz/gen_ref/slice.nii.gz is 20.932278 degrees from plumb. | |
| 200301-21:46:43,420 nipype.interface INFO: | |
| stderr 2020-03-01T21:46:43.419977:++ Coarse del was 10, replaced with 6 | |
| 2020-03-01 21:46:43,420 nipype.interface:INFO stderr 2020-03-01T21:46:43.419977:++ Coarse del was 10, replaced with 6 | |
| 200301-21:46:48,24 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.funcMRIQC.ReportsWorkflow.SpikesFinderBgMask". | |
| 2020-03-01 21:46:48,024 nipype.workflow:INFO [Node] Finished "workflow_enumerator.funcMRIQC.ReportsWorkflow.SpikesFinderBgMask". | |
| 200301-21:46:48,467 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.AirMaskWorkflow.RotationMask" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT2w/AirMaskWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/RotationMask". | |
| 2020-03-01 21:46:48,467 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.AirMaskWorkflow.RotationMask" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT2w/AirMaskWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/RotationMask". | |
| 200301-21:46:48,470 nipype.workflow INFO: | |
| [Node] Running "RotationMask" ("mriqc.interfaces.anatomical.RotationMask") | |
| 2020-03-01 21:46:48,470 nipype.workflow:INFO [Node] Running "RotationMask" ("mriqc.interfaces.anatomical.RotationMask") | |
| 200301-21:46:52,231 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT2w.AirMaskWorkflow.RotationMask". | |
| 2020-03-01 21:46:52,231 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT2w.AirMaskWorkflow.RotationMask". | |
| 200301-21:46:52,459 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.AFNISkullStripWorkflow.inu_n4" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT2w/AFNISkullStripWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/inu_n4". | |
| 2020-03-01 21:46:52,459 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.AFNISkullStripWorkflow.inu_n4" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT2w/AFNISkullStripWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/inu_n4". | |
| 200301-21:46:52,462 nipype.workflow INFO: | |
| [Node] Running "inu_n4" ("nipype.interfaces.ants.segmentation.N4BiasFieldCorrection"), a CommandLine Interface with command: | |
| N4BiasFieldCorrection -d 3 --input-image /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT2w/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/conform/sub-01_ses-01_T2w_conformed.nii.gz --output [ sub-01_ses-01_T2w_conformed_corrected.nii.gz, sub-01_ses-01_T2w_conformed_bias.nii.gz ] | |
| 2020-03-01 21:46:52,462 nipype.workflow:INFO [Node] Running "inu_n4" ("nipype.interfaces.ants.segmentation.N4BiasFieldCorrection"), a CommandLine Interface with command: | |
| N4BiasFieldCorrection -d 3 --input-image /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT2w/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/conform/sub-01_ses-01_T2w_conformed.nii.gz --output [ sub-01_ses-01_T2w_conformed_corrected.nii.gz, sub-01_ses-01_T2w_conformed_bias.nii.gz ] | |
| 200301-21:47:57,665 nipype.interface INFO: | |
| stderr 2020-03-01T21:47:57.665802:++ Max displacement in automask = 1.03 (mm) at sub-brick 16 | |
| 2020-03-01 21:47:57,665 nipype.interface:INFO stderr 2020-03-01T21:47:57.665802:++ Max displacement in automask = 1.03 (mm) at sub-brick 16 | |
| 200301-21:47:57,666 nipype.interface INFO: | |
| stderr 2020-03-01T21:47:57.666042:++ Max delta displ in automask = 0.79 (mm) at sub-brick 17 | |
| 2020-03-01 21:47:57,666 nipype.interface:INFO stderr 2020-03-01T21:47:57.666042:++ Max delta displ in automask = 0.79 (mm) at sub-brick 17 | |
| 200301-21:48:01,883 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.funcMRIQC.fMRI_HMC_afni.gen_ref". | |
| 2020-03-01 21:48:01,883 nipype.workflow:INFO [Node] Finished "workflow_enumerator.funcMRIQC.fMRI_HMC_afni.gen_ref". | |
| 200301-21:48:02,541 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.funcMRIQC.fMRI_HMC_afni.motion_correct" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/funcMRIQC/fMRI_HMC_afni/_in_file_..data..sub-01..ses-01..func..sub-01_ses-01_task-Stroop_run-01_bold.nii.gz/motion_correct". | |
| 2020-03-01 21:48:02,541 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.funcMRIQC.fMRI_HMC_afni.motion_correct" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/funcMRIQC/fMRI_HMC_afni/_in_file_..data..sub-01..ses-01..func..sub-01_ses-01_task-Stroop_run-01_bold.nii.gz/motion_correct". | |
| 200301-21:48:02,544 nipype.workflow INFO: | |
| [Node] Running "motion_correct" ("nipype.interfaces.afni.preprocess.Volreg"), a CommandLine Interface with command: | |
| 3dvolreg -Fourier -twopass -1Dfile sub-01_ses-01_task-Stroop_run-01_bold_valid.1D -1Dmatrix_save sub-01_ses-01_task-Stroop_run-01_bold_valid.aff12.1D -prefix sub-01_ses-01_task-Stroop_run-01_bold_valid_volreg.nii.gz -base /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/funcMRIQC/fMRI_HMC_afni/_in_file_..data..sub-01..ses-01..func..sub-01_ses-01_task-Stroop_run-01_bold.nii.gz/gen_ref/ref_image.nii.gz -zpad 4 -maxdisp1D sub-01_ses-01_task-Stroop_run-01_bold_valid_md.1D /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/funcMRIQC/fMRI_HMC_afni/_in_file_..data..sub-01..ses-01..func..sub-01_ses-01_task-Stroop_run-01_bold.nii.gz/motion_correct/sub-01_ses-01_task-Stroop_run-01_bold_valid.nii.gz | |
| 2020-03-01 21:48:02,544 nipype.workflow:INFO [Node] Running "motion_correct" ("nipype.interfaces.afni.preprocess.Volreg"), a CommandLine Interface with command: | |
| 3dvolreg -Fourier -twopass -1Dfile sub-01_ses-01_task-Stroop_run-01_bold_valid.1D -1Dmatrix_save sub-01_ses-01_task-Stroop_run-01_bold_valid.aff12.1D -prefix sub-01_ses-01_task-Stroop_run-01_bold_valid_volreg.nii.gz -base /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/funcMRIQC/fMRI_HMC_afni/_in_file_..data..sub-01..ses-01..func..sub-01_ses-01_task-Stroop_run-01_bold.nii.gz/gen_ref/ref_image.nii.gz -zpad 4 -maxdisp1D sub-01_ses-01_task-Stroop_run-01_bold_valid_md.1D /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/funcMRIQC/fMRI_HMC_afni/_in_file_..data..sub-01..ses-01..func..sub-01_ses-01_task-Stroop_run-01_bold.nii.gz/motion_correct/sub-01_ses-01_task-Stroop_run-01_bold_valid.nii.gz | |
| 200301-21:52:49,95 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT1w.AFNISkullStripWorkflow.inu_n4". | |
| 2020-03-01 21:52:49,095 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT1w.AFNISkullStripWorkflow.inu_n4". | |
| 200301-21:52:50,827 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.HeadMaskWorkflow.fsl_bet" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT1w/HeadMaskWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/fsl_bet". | |
| 2020-03-01 21:52:50,827 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.HeadMaskWorkflow.fsl_bet" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT1w/HeadMaskWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/fsl_bet". | |
| 200301-21:52:50,830 nipype.workflow INFO: | |
| [Node] Running "fsl_bet" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command: | |
| bet /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT1w/AFNISkullStripWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/inu_n4/sub-01_ses-01_T1w_conformed_corrected.nii.gz /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT1w/HeadMaskWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/fsl_bet/sub-01_ses-01_T1w_conformed_corrected_brain.nii.gz -A | |
| 2020-03-01 21:52:50,830 nipype.workflow:INFO [Node] Running "fsl_bet" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command: | |
| bet /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT1w/AFNISkullStripWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/inu_n4/sub-01_ses-01_T1w_conformed_corrected.nii.gz /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT1w/HeadMaskWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/fsl_bet/sub-01_ses-01_T1w_conformed_corrected_brain.nii.gz -A | |
| 200301-21:56:23,82 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT1w.HeadMaskWorkflow.fsl_bet". | |
| 2020-03-01 21:56:23,082 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT1w.HeadMaskWorkflow.fsl_bet". | |
| 200301-21:56:25,39 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.AFNISkullStripWorkflow.skullstrip" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT1w/AFNISkullStripWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/skullstrip". | |
| 2020-03-01 21:56:25,039 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.AFNISkullStripWorkflow.skullstrip" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT1w/AFNISkullStripWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/skullstrip". | |
| 200301-21:56:25,42 nipype.workflow INFO: | |
| [Node] Running "skullstrip" ("nipype.interfaces.afni.preprocess.SkullStrip"), a CommandLine Interface with command: | |
| 3dSkullStrip -input /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT1w/AFNISkullStripWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/skullstrip/sub-01_ses-01_T1w_conformed_corrected.nii.gz -prefix sub-01_ses-01_T1w_conformed_corrected_skullstrip.nii.gz | |
| 2020-03-01 21:56:25,042 nipype.workflow:INFO [Node] Running "skullstrip" ("nipype.interfaces.afni.preprocess.SkullStrip"), a CommandLine Interface with command: | |
| 3dSkullStrip -input /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT1w/AFNISkullStripWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/skullstrip/sub-01_ses-01_T1w_conformed_corrected.nii.gz -prefix sub-01_ses-01_T1w_conformed_corrected_skullstrip.nii.gz | |
| 200301-21:58:22,395 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT2w.AFNISkullStripWorkflow.inu_n4". | |
| 2020-03-01 21:58:22,395 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT2w.AFNISkullStripWorkflow.inu_n4". | |
| 200301-21:58:23,157 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.HeadMaskWorkflow.fsl_bet" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT2w/HeadMaskWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/fsl_bet". | |
| 2020-03-01 21:58:23,157 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.HeadMaskWorkflow.fsl_bet" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT2w/HeadMaskWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/fsl_bet". | |
| 200301-21:58:23,160 nipype.workflow INFO: | |
| [Node] Running "fsl_bet" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command: | |
| bet /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT2w/AFNISkullStripWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/inu_n4/sub-01_ses-01_T2w_conformed_corrected.nii.gz /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT2w/HeadMaskWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/fsl_bet/sub-01_ses-01_T2w_conformed_corrected_brain.nii.gz -A | |
| 2020-03-01 21:58:23,160 nipype.workflow:INFO [Node] Running "fsl_bet" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command: | |
| bet /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT2w/AFNISkullStripWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/inu_n4/sub-01_ses-01_T2w_conformed_corrected.nii.gz /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT2w/HeadMaskWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/fsl_bet/sub-01_ses-01_T2w_conformed_corrected_brain.nii.gz -A | |
| 200301-21:58:35,933 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT1w.AFNISkullStripWorkflow.skullstrip". | |
| 2020-03-01 21:58:35,933 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT1w.AFNISkullStripWorkflow.skullstrip". | |
| 200301-21:58:37,171 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.AFNISkullStripWorkflow.sstrip_orig_vol" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT1w/AFNISkullStripWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/sstrip_orig_vol". | |
| 2020-03-01 21:58:37,171 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.AFNISkullStripWorkflow.sstrip_orig_vol" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT1w/AFNISkullStripWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/sstrip_orig_vol". | |
| 200301-21:58:37,174 nipype.workflow INFO: | |
| [Node] Running "sstrip_orig_vol" ("nipype.interfaces.afni.utils.Calc"), a CommandLine Interface with command: | |
| 3dcalc -a /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT1w/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/conform/sub-01_ses-01_T1w_conformed.nii.gz -b /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT1w/AFNISkullStripWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/skullstrip/sub-01_ses-01_T1w_conformed_corrected_skullstrip.nii.gz -expr "a*step(b)" -prefix sub-01_ses-01_T1w_conformed_calc.nii.gz | |
| 2020-03-01 21:58:37,174 nipype.workflow:INFO [Node] Running "sstrip_orig_vol" ("nipype.interfaces.afni.utils.Calc"), a CommandLine Interface with command: | |
| 3dcalc -a /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT1w/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/conform/sub-01_ses-01_T1w_conformed.nii.gz -b /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT1w/AFNISkullStripWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/skullstrip/sub-01_ses-01_T1w_conformed_corrected_skullstrip.nii.gz -expr "a*step(b)" -prefix sub-01_ses-01_T1w_conformed_calc.nii.gz | |
| 200301-21:58:41,281 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT1w.AFNISkullStripWorkflow.sstrip_orig_vol". | |
| 2020-03-01 21:58:41,281 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT1w.AFNISkullStripWorkflow.sstrip_orig_vol". | |
| 200301-21:58:43,192 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.segmentation" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT1w/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/segmentation". | |
| 2020-03-01 21:58:43,192 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.segmentation" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT1w/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/segmentation". | |
| 200301-21:58:43,196 nipype.workflow INFO: | |
| [Node] Running "segmentation" ("nipype.interfaces.fsl.preprocess.FAST"), a CommandLine Interface with command: | |
| fast -t 1 -o segment -g -S 1 /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT1w/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/segmentation/sub-01_ses-01_T1w_conformed_calc.nii.gz | |
| 2020-03-01 21:58:43,196 nipype.workflow:INFO [Node] Running "segmentation" ("nipype.interfaces.fsl.preprocess.FAST"), a CommandLine Interface with command: | |
| fast -t 1 -o segment -g -S 1 /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT1w/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/segmentation/sub-01_ses-01_T1w_conformed_calc.nii.gz | |
| 200301-22:01:09,650 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT2w.HeadMaskWorkflow.fsl_bet". | |
| 2020-03-01 22:01:09,650 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT2w.HeadMaskWorkflow.fsl_bet". | |
| 200301-22:01:11,321 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.AFNISkullStripWorkflow.binarize" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT1w/AFNISkullStripWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/binarize". | |
| 2020-03-01 22:01:11,321 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.AFNISkullStripWorkflow.binarize" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT1w/AFNISkullStripWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/binarize". | |
| 200301-22:01:11,325 nipype.workflow INFO: | |
| [Node] Running "binarize" ("nipype.interfaces.fsl.maths.Threshold"), a CommandLine Interface with command: | |
| fslmaths /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT1w/AFNISkullStripWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/sstrip_orig_vol/sub-01_ses-01_T1w_conformed_calc.nii.gz -thr 0.0010000000 -bin /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT1w/AFNISkullStripWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/binarize/sub-01_ses-01_T1w_conformed_calc_thresh.nii.gz | |
| 2020-03-01 22:01:11,325 nipype.workflow:INFO [Node] Running "binarize" ("nipype.interfaces.fsl.maths.Threshold"), a CommandLine Interface with command: | |
| fslmaths /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT1w/AFNISkullStripWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/sstrip_orig_vol/sub-01_ses-01_T1w_conformed_calc.nii.gz -thr 0.0010000000 -bin /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT1w/AFNISkullStripWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/binarize/sub-01_ses-01_T1w_conformed_calc_thresh.nii.gz | |
| 200301-22:01:14,213 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT1w.AFNISkullStripWorkflow.binarize". | |
| 2020-03-01 22:01:14,213 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT1w.AFNISkullStripWorkflow.binarize". | |
| 200301-22:01:15,325 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.ReportsWorkflow.PlotMosaicZoomed" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT1w/ReportsWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/PlotMosaicZoomed". | |
| 2020-03-01 22:01:15,325 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.ReportsWorkflow.PlotMosaicZoomed" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT1w/ReportsWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/PlotMosaicZoomed". | |
| 200301-22:01:15,327 nipype.workflow INFO: | |
| [Node] Running "PlotMosaicZoomed" ("mriqc.interfaces.viz.PlotMosaic") | |
| 2020-03-01 22:01:15,327 nipype.workflow:INFO [Node] Running "PlotMosaicZoomed" ("mriqc.interfaces.viz.PlotMosaic") | |
| 200301-22:01:38,833 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT1w.ReportsWorkflow.PlotMosaicZoomed". | |
| 2020-03-01 22:01:38,833 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT1w.ReportsWorkflow.PlotMosaicZoomed". | |
| 200301-22:01:39,360 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.ReportsWorkflow.MergePlots" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT1w/ReportsWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/MergePlots". | |
| 2020-03-01 22:01:39,360 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.ReportsWorkflow.MergePlots" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT1w/ReportsWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/MergePlots". | |
| 200301-22:01:39,363 nipype.workflow INFO: | |
| [Node] Running "MergePlots" ("nipype.interfaces.utility.base.Merge") | |
| 2020-03-01 22:01:39,363 nipype.workflow:INFO [Node] Running "MergePlots" ("nipype.interfaces.utility.base.Merge") | |
| 200301-22:01:39,366 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT1w.ReportsWorkflow.MergePlots". | |
| 2020-03-01 22:01:39,366 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT1w.ReportsWorkflow.MergePlots". | |
| 200301-22:01:41,348 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.ComputeIQMs.smoothness" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT1w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/smoothness". | |
| 2020-03-01 22:01:41,348 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.ComputeIQMs.smoothness" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT1w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/smoothness". | |
| 200301-22:01:41,351 nipype.workflow INFO: | |
| [Node] Running "smoothness" ("nipype.interfaces.afni.utils.FWHMx"), a CommandLine Interface with command: | |
| 3dFWHMx -ShowMeClassicFWHM -combine -detrend -input /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT1w/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/conform/sub-01_ses-01_T1w_conformed.nii.gz -mask /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT1w/AFNISkullStripWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/binarize/sub-01_ses-01_T1w_conformed_calc_thresh.nii.gz -detprefix sub-01_ses-01_T1w_conformed_detrend -out sub-01_ses-01_T1w_conformed_subbricks.out > sub-01_ses-01_T1w_conformed_fwhmx.out | |
| 2020-03-01 22:01:41,351 nipype.workflow:INFO [Node] Running "smoothness" ("nipype.interfaces.afni.utils.FWHMx"), a CommandLine Interface with command: | |
| 3dFWHMx -ShowMeClassicFWHM -combine -detrend -input /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT1w/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/conform/sub-01_ses-01_T1w_conformed.nii.gz -mask /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT1w/AFNISkullStripWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/binarize/sub-01_ses-01_T1w_conformed_calc_thresh.nii.gz -detprefix sub-01_ses-01_T1w_conformed_detrend -out sub-01_ses-01_T1w_conformed_subbricks.out > sub-01_ses-01_T1w_conformed_fwhmx.out | |
| 200301-22:02:03,850 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT1w.ComputeIQMs.smoothness". | |
| 2020-03-01 22:02:03,850 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT1w.ComputeIQMs.smoothness". | |
| 200301-22:02:05,368 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.SpatialNormalization.SpatialNormalization" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT1w/SpatialNormalization/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/SpatialNormalization". | |
| 2020-03-01 22:02:05,368 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.SpatialNormalization.SpatialNormalization" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT1w/SpatialNormalization/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/SpatialNormalization". | |
| 200301-22:02:05,371 nipype.workflow INFO: | |
| [Node] Running "SpatialNormalization" ("niworkflows.interfaces.registration.RobustMNINormalizationRPT") | |
| 2020-03-01 22:02:05,371 nipype.workflow:INFO [Node] Running "SpatialNormalization" ("niworkflows.interfaces.registration.RobustMNINormalizationRPT") | |
| 2020-03-01 22:02:08,830 niworkflows:INFO Estimating initial transform using AffineInitializer | |
| 2020-03-01 22:06:44,872 niworkflows:INFO Loading settings from file /usr/local/miniconda/lib/python3.7/site-packages/niworkflows/data/t1w-mni_registration_fast_000.json. | |
| 2020-03-01 22:06:44,873 niworkflows:INFO Retry #1, commandline: | |
| antsRegistration --collapse-output-transforms 1 --dimensionality 3 --float 0 --initial-moving-transform [ /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT1w/SpatialNormalization/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/SpatialNormalization/transform.mat, 0 ] --initialize-transforms-per-stage 0 --interpolation LanczosWindowedSinc --output [ ants_t1_to_mni, ants_t1_to_mni_Warped.nii.gz ] --transform Rigid[ 0.01 ] --metric Mattes[ /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT1w/SpatialNormalization/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/SpatialNormalization/fixed_masked.nii.gz, /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT1w/SpatialNormalization/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/SpatialNormalization/moving_masked.nii.gz, 1, 32, Random, 0.15 ] --convergence [ 1000, 1e-06, 20 ] --smoothing-sigmas 4.0vox --shrink-factors 4 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --transform Affine[ 0.08 ] --metric Mattes[ /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT1w/SpatialNormalization/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/SpatialNormalization/fixed_masked.nii.gz, /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT1w/SpatialNormalization/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/SpatialNormalization/moving_masked.nii.gz, 1, 32, Regular, 0.15 ] --convergence [ 500x250x100, 1e-06, 20 ] --smoothing-sigmas 4.0x2.0x0.0vox --shrink-factors 4x2x1 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --transform SyN[ 0.1, 3.0, 0.0 ] --metric Mattes[ /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT1w/SpatialNormalization/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/SpatialNormalization/fixed_masked.nii.gz, /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT1w/SpatialNormalization/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/SpatialNormalization/moving_masked.nii.gz, 1, 56, Regular, 0.25 ] --convergence [ 50x20, 1e-06, 10 ] --smoothing-sigmas 1.0x0.0vox --shrink-factors 2x1 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --winsorize-image-intensities [ 0.0, 1.0 ] --write-composite-transform 1 | |
| 200301-22:09:58,508 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.funcMRIQC.fMRI_HMC_afni.motion_correct". | |
| 2020-03-01 22:09:58,508 nipype.workflow:INFO [Node] Finished "workflow_enumerator.funcMRIQC.fMRI_HMC_afni.motion_correct". | |
| 200301-22:09:59,844 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.funcMRIQC.ComputeIQMs.quality" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/funcMRIQC/ComputeIQMs/_in_file_..data..sub-01..ses-01..func..sub-01_ses-01_task-Stroop_run-01_bold.nii.gz/quality". | |
| 2020-03-01 22:09:59,844 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.funcMRIQC.ComputeIQMs.quality" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/funcMRIQC/ComputeIQMs/_in_file_..data..sub-01..ses-01..func..sub-01_ses-01_task-Stroop_run-01_bold.nii.gz/quality". | |
| 200301-22:09:59,847 nipype.workflow INFO: | |
| [Node] Running "quality" ("nipype.interfaces.afni.preprocess.QualityIndex"), a CommandLine Interface with command: | |
| 3dTqual -automask /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/funcMRIQC/fMRI_HMC_afni/_in_file_..data..sub-01..ses-01..func..sub-01_ses-01_task-Stroop_run-01_bold.nii.gz/motion_correct/sub-01_ses-01_task-Stroop_run-01_bold_valid_volreg.nii.gz > sub-01_ses-01_task-Stroop_run-01_bold_valid_volreg_tqual | |
| 2020-03-01 22:09:59,847 nipype.workflow:INFO [Node] Running "quality" ("nipype.interfaces.afni.preprocess.QualityIndex"), a CommandLine Interface with command: | |
| 3dTqual -automask /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/funcMRIQC/fMRI_HMC_afni/_in_file_..data..sub-01..ses-01..func..sub-01_ses-01_task-Stroop_run-01_bold.nii.gz/motion_correct/sub-01_ses-01_task-Stroop_run-01_bold_valid_volreg.nii.gz > sub-01_ses-01_task-Stroop_run-01_bold_valid_volreg_tqual | |
| 200301-22:10:26,205 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.funcMRIQC.ComputeIQMs.quality". | |
| 2020-03-01 22:10:26,205 nipype.workflow:INFO [Node] Finished "workflow_enumerator.funcMRIQC.ComputeIQMs.quality". | |
| 200301-22:10:27,870 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.funcMRIQC.compute_tsnr" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/funcMRIQC/_in_file_..data..sub-01..ses-01..func..sub-01_ses-01_task-Stroop_run-01_bold.nii.gz/compute_tsnr". | |
| 2020-03-01 22:10:27,870 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.funcMRIQC.compute_tsnr" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/funcMRIQC/_in_file_..data..sub-01..ses-01..func..sub-01_ses-01_task-Stroop_run-01_bold.nii.gz/compute_tsnr". | |
| 200301-22:10:27,874 nipype.workflow INFO: | |
| [Node] Running "compute_tsnr" ("nipype.algorithms.confounds.TSNR") | |
| 2020-03-01 22:10:27,874 nipype.workflow:INFO [Node] Running "compute_tsnr" ("nipype.algorithms.confounds.TSNR") | |
| 200301-22:10:39,765 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.funcMRIQC.compute_tsnr". | |
| 2020-03-01 22:10:39,765 nipype.workflow:INFO [Node] Finished "workflow_enumerator.funcMRIQC.compute_tsnr". | |
| 200301-22:10:41,883 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.funcMRIQC.ReportsWorkflow.PlotMosaicSD" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/funcMRIQC/ReportsWorkflow/_in_file_..data..sub-01..ses-01..func..sub-01_ses-01_task-Stroop_run-01_bold.nii.gz/PlotMosaicSD". | |
| 2020-03-01 22:10:41,883 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.funcMRIQC.ReportsWorkflow.PlotMosaicSD" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/funcMRIQC/ReportsWorkflow/_in_file_..data..sub-01..ses-01..func..sub-01_ses-01_task-Stroop_run-01_bold.nii.gz/PlotMosaicSD". | |
| 200301-22:10:41,886 nipype.workflow INFO: | |
| [Node] Running "PlotMosaicSD" ("mriqc.interfaces.viz.PlotMosaic") | |
| 2020-03-01 22:10:41,886 nipype.workflow:INFO [Node] Running "PlotMosaicSD" ("mriqc.interfaces.viz.PlotMosaic") | |
| 200301-22:10:59,699 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.funcMRIQC.ReportsWorkflow.PlotMosaicSD". | |
| 2020-03-01 22:10:59,699 nipype.workflow:INFO [Node] Finished "workflow_enumerator.funcMRIQC.ReportsWorkflow.PlotMosaicSD". | |
| 200301-22:10:59,902 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.funcMRIQC.mean" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/funcMRIQC/_in_file_..data..sub-01..ses-01..func..sub-01_ses-01_task-Stroop_run-01_bold.nii.gz/mean". | |
| 2020-03-01 22:10:59,902 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.funcMRIQC.mean" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/funcMRIQC/_in_file_..data..sub-01..ses-01..func..sub-01_ses-01_task-Stroop_run-01_bold.nii.gz/mean". | |
| 200301-22:10:59,905 nipype.workflow INFO: | |
| [Node] Running "mean" ("nipype.interfaces.afni.utils.TStat"), a CommandLine Interface with command: | |
| 3dTstat -mean -prefix sub-01_ses-01_task-Stroop_run-01_bold_valid_volreg_tstat.nii.gz /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/funcMRIQC/_in_file_..data..sub-01..ses-01..func..sub-01_ses-01_task-Stroop_run-01_bold.nii.gz/mean/sub-01_ses-01_task-Stroop_run-01_bold_valid_volreg.nii.gz | |
| 2020-03-01 22:10:59,905 nipype.workflow:INFO [Node] Running "mean" ("nipype.interfaces.afni.utils.TStat"), a CommandLine Interface with command: | |
| 3dTstat -mean -prefix sub-01_ses-01_task-Stroop_run-01_bold_valid_volreg_tstat.nii.gz /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/funcMRIQC/_in_file_..data..sub-01..ses-01..func..sub-01_ses-01_task-Stroop_run-01_bold.nii.gz/mean/sub-01_ses-01_task-Stroop_run-01_bold_valid_volreg.nii.gz | |
| 200301-22:11:11,289 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.funcMRIQC.mean". | |
| 2020-03-01 22:11:11,289 nipype.workflow:INFO [Node] Finished "workflow_enumerator.funcMRIQC.mean". | |
| 200301-22:11:11,930 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.funcMRIQC.ReportsWorkflow.PlotMosaicMean" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/funcMRIQC/ReportsWorkflow/_in_file_..data..sub-01..ses-01..func..sub-01_ses-01_task-Stroop_run-01_bold.nii.gz/PlotMosaicMean". | |
| 2020-03-01 22:11:11,930 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.funcMRIQC.ReportsWorkflow.PlotMosaicMean" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/funcMRIQC/ReportsWorkflow/_in_file_..data..sub-01..ses-01..func..sub-01_ses-01_task-Stroop_run-01_bold.nii.gz/PlotMosaicMean". | |
| 200301-22:11:11,932 nipype.workflow INFO: | |
| [Node] Running "PlotMosaicMean" ("mriqc.interfaces.viz.PlotMosaic") | |
| 2020-03-01 22:11:11,932 nipype.workflow:INFO [Node] Running "PlotMosaicMean" ("mriqc.interfaces.viz.PlotMosaic") | |
| 200301-22:11:24,284 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT1w.segmentation". | |
| 2020-03-01 22:11:24,284 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT1w.segmentation". | |
| 200301-22:11:25,926 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.funcMRIQC.SpatialNormalization.SharpenEPI" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/funcMRIQC/SpatialNormalization/_in_file_..data..sub-01..ses-01..func..sub-01_ses-01_task-Stroop_run-01_bold.nii.gz/SharpenEPI". | |
| 2020-03-01 22:11:25,926 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.funcMRIQC.SpatialNormalization.SharpenEPI" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/funcMRIQC/SpatialNormalization/_in_file_..data..sub-01..ses-01..func..sub-01_ses-01_task-Stroop_run-01_bold.nii.gz/SharpenEPI". | |
| 200301-22:11:25,929 nipype.workflow INFO: | |
| [Node] Running "SharpenEPI" ("nipype.interfaces.ants.segmentation.N4BiasFieldCorrection"), a CommandLine Interface with command: | |
| N4BiasFieldCorrection -d 3 --input-image /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/funcMRIQC/_in_file_..data..sub-01..ses-01..func..sub-01_ses-01_task-Stroop_run-01_bold.nii.gz/mean/sub-01_ses-01_task-Stroop_run-01_bold_valid_volreg_tstat.nii.gz --output sub-01_ses-01_task-Stroop_run-01_bold_valid_volreg_tstat_corrected.nii.gz | |
| 2020-03-01 22:11:25,929 nipype.workflow:INFO [Node] Running "SharpenEPI" ("nipype.interfaces.ants.segmentation.N4BiasFieldCorrection"), a CommandLine Interface with command: | |
| N4BiasFieldCorrection -d 3 --input-image /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/funcMRIQC/_in_file_..data..sub-01..ses-01..func..sub-01_ses-01_task-Stroop_run-01_bold.nii.gz/mean/sub-01_ses-01_task-Stroop_run-01_bold_valid_volreg_tstat.nii.gz --output sub-01_ses-01_task-Stroop_run-01_bold_valid_volreg_tstat_corrected.nii.gz | |
| 200301-22:11:26,193 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.funcMRIQC.ReportsWorkflow.PlotMosaicMean". | |
| 2020-03-01 22:11:26,193 nipype.workflow:INFO [Node] Finished "workflow_enumerator.funcMRIQC.ReportsWorkflow.PlotMosaicMean". | |
| 2020-03-01 22:11:27,209 niworkflows:INFO Successful spatial normalization (retry #1). | |
| 200301-22:11:27,932 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.funcMRIQC.fMRIBrainMask.bet_msk" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..data..sub-01..ses-01..func..sub-01_ses-01_task-Stroop_run-01_bold.nii.gz/bet_msk". | |
| 2020-03-01 22:11:27,932 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.funcMRIQC.fMRIBrainMask.bet_msk" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..data..sub-01..ses-01..func..sub-01_ses-01_task-Stroop_run-01_bold.nii.gz/bet_msk". | |
| 200301-22:11:27,935 nipype.workflow INFO: | |
| [Node] Running "bet_msk" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command: | |
| bet /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/funcMRIQC/_in_file_..data..sub-01..ses-01..func..sub-01_ses-01_task-Stroop_run-01_bold.nii.gz/mean/sub-01_ses-01_task-Stroop_run-01_bold_valid_volreg_tstat.nii.gz /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..data..sub-01..ses-01..func..sub-01_ses-01_task-Stroop_run-01_bold.nii.gz/bet_msk/sub-01_ses-01_task-Stroop_run-01_bold_valid_volreg_tstat_brain.nii.gz -F -m | |
| 2020-03-01 22:11:27,935 nipype.workflow:INFO [Node] Running "bet_msk" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command: | |
| bet /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/funcMRIQC/_in_file_..data..sub-01..ses-01..func..sub-01_ses-01_task-Stroop_run-01_bold.nii.gz/mean/sub-01_ses-01_task-Stroop_run-01_bold_valid_volreg_tstat.nii.gz /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..data..sub-01..ses-01..func..sub-01_ses-01_task-Stroop_run-01_bold.nii.gz/bet_msk/sub-01_ses-01_task-Stroop_run-01_bold_valid_volreg_tstat_brain.nii.gz -F -m | |
| 2020-03-01 22:11:33,017 niworkflows:INFO Report - setting fixed (/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT1w/SpatialNormalization/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/SpatialNormalization/fixed_masked.nii.gz) and moving (/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT1w/SpatialNormalization/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/SpatialNormalization/ants_t1_to_mni_Warped.nii.gz) images | |
| 2020-03-01 22:11:33,017 niworkflows:INFO Generating visual report | |
| 200301-22:11:33,384 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.funcMRIQC.fMRIBrainMask.bet_msk". | |
| 2020-03-01 22:11:33,384 nipype.workflow:INFO [Node] Finished "workflow_enumerator.funcMRIQC.fMRIBrainMask.bet_msk". | |
| 200301-22:11:33,937 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.funcMRIQC.fMRIBrainMask.erode" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..data..sub-01..ses-01..func..sub-01_ses-01_task-Stroop_run-01_bold.nii.gz/erode". | |
| 2020-03-01 22:11:33,937 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.funcMRIQC.fMRIBrainMask.erode" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..data..sub-01..ses-01..func..sub-01_ses-01_task-Stroop_run-01_bold.nii.gz/erode". | |
| 200301-22:11:33,940 nipype.workflow INFO: | |
| [Node] Running "erode" ("nipype.interfaces.fsl.maths.ErodeImage"), a CommandLine Interface with command: | |
| fslmaths /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..data..sub-01..ses-01..func..sub-01_ses-01_task-Stroop_run-01_bold.nii.gz/bet_msk/sub-01_ses-01_task-Stroop_run-01_bold_valid_volreg_tstat_brain_mask.nii.gz -ero /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..data..sub-01..ses-01..func..sub-01_ses-01_task-Stroop_run-01_bold.nii.gz/erode/sub-01_ses-01_task-Stroop_run-01_bold_valid_volreg_tstat_brain_mask_ero.nii.gz | |
| 2020-03-01 22:11:33,940 nipype.workflow:INFO [Node] Running "erode" ("nipype.interfaces.fsl.maths.ErodeImage"), a CommandLine Interface with command: | |
| fslmaths /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..data..sub-01..ses-01..func..sub-01_ses-01_task-Stroop_run-01_bold.nii.gz/bet_msk/sub-01_ses-01_task-Stroop_run-01_bold_valid_volreg_tstat_brain_mask.nii.gz -ero /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..data..sub-01..ses-01..func..sub-01_ses-01_task-Stroop_run-01_bold.nii.gz/erode/sub-01_ses-01_task-Stroop_run-01_bold_valid_volreg_tstat_brain_mask_ero.nii.gz | |
| 200301-22:11:35,714 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.funcMRIQC.fMRIBrainMask.erode". | |
| 2020-03-01 22:11:35,714 nipype.workflow:INFO [Node] Finished "workflow_enumerator.funcMRIQC.fMRIBrainMask.erode". | |
| 200301-22:11:35,754 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.funcMRIQC.SpatialNormalization.SharpenEPI". | |
| 2020-03-01 22:11:35,754 nipype.workflow:INFO [Node] Finished "workflow_enumerator.funcMRIQC.SpatialNormalization.SharpenEPI". | |
| 200301-22:11:35,881 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.funcMRIQC.ComputeIQMs.gcor" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/funcMRIQC/ComputeIQMs/_in_file_..data..sub-01..ses-01..func..sub-01_ses-01_task-Stroop_run-01_bold.nii.gz/gcor". | |
| 2020-03-01 22:11:35,881 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.funcMRIQC.ComputeIQMs.gcor" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/funcMRIQC/ComputeIQMs/_in_file_..data..sub-01..ses-01..func..sub-01_ses-01_task-Stroop_run-01_bold.nii.gz/gcor". | |
| 200301-22:11:35,884 nipype.workflow INFO: | |
| [Node] Running "gcor" ("mriqc.interfaces.transitional.GCOR"), a CommandLine Interface with command: | |
| @compute_gcor -mask /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/funcMRIQC/ComputeIQMs/_in_file_..data..sub-01..ses-01..func..sub-01_ses-01_task-Stroop_run-01_bold.nii.gz/gcor/sub-01_ses-01_task-Stroop_run-01_bold_valid_volreg_tstat_brain_mask_ero.nii.gz -input /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/funcMRIQC/ComputeIQMs/_in_file_..data..sub-01..ses-01..func..sub-01_ses-01_task-Stroop_run-01_bold.nii.gz/gcor/sub-01_ses-01_task-Stroop_run-01_bold_valid_volreg.nii.gz | |
| 2020-03-01 22:11:35,884 nipype.workflow:INFO [Node] Running "gcor" ("mriqc.interfaces.transitional.GCOR"), a CommandLine Interface with command: | |
| @compute_gcor -mask /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/funcMRIQC/ComputeIQMs/_in_file_..data..sub-01..ses-01..func..sub-01_ses-01_task-Stroop_run-01_bold.nii.gz/gcor/sub-01_ses-01_task-Stroop_run-01_bold_valid_volreg_tstat_brain_mask_ero.nii.gz -input /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/funcMRIQC/ComputeIQMs/_in_file_..data..sub-01..ses-01..func..sub-01_ses-01_task-Stroop_run-01_bold.nii.gz/gcor/sub-01_ses-01_task-Stroop_run-01_bold_valid_volreg.nii.gz | |
| 200301-22:11:35,894 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.funcMRIQC.ComputeIQMs.outliers" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/funcMRIQC/ComputeIQMs/_in_file_..data..sub-01..ses-01..func..sub-01_ses-01_task-Stroop_run-01_bold.nii.gz/outliers". | |
| 2020-03-01 22:11:35,894 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.funcMRIQC.ComputeIQMs.outliers" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/funcMRIQC/ComputeIQMs/_in_file_..data..sub-01..ses-01..func..sub-01_ses-01_task-Stroop_run-01_bold.nii.gz/outliers". | |
| 200301-22:11:35,897 nipype.workflow INFO: | |
| [Node] Running "outliers" ("nipype.interfaces.afni.preprocess.OutlierCount"), a CommandLine Interface with command: | |
| 3dToutcount -fraction -mask /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..data..sub-01..ses-01..func..sub-01_ses-01_task-Stroop_run-01_bold.nii.gz/erode/sub-01_ses-01_task-Stroop_run-01_bold_valid_volreg_tstat_brain_mask_ero.nii.gz -qthr 0.00100 /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/funcMRIQC/fMRI_HMC_afni/_in_file_..data..sub-01..ses-01..func..sub-01_ses-01_task-Stroop_run-01_bold.nii.gz/motion_correct/sub-01_ses-01_task-Stroop_run-01_bold_valid_volreg.nii.gz | |
| 2020-03-01 22:11:35,897 nipype.workflow:INFO [Node] Running "outliers" ("nipype.interfaces.afni.preprocess.OutlierCount"), a CommandLine Interface with command: | |
| 3dToutcount -fraction -mask /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..data..sub-01..ses-01..func..sub-01_ses-01_task-Stroop_run-01_bold.nii.gz/erode/sub-01_ses-01_task-Stroop_run-01_bold_valid_volreg_tstat_brain_mask_ero.nii.gz -qthr 0.00100 /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/funcMRIQC/fMRI_HMC_afni/_in_file_..data..sub-01..ses-01..func..sub-01_ses-01_task-Stroop_run-01_bold.nii.gz/motion_correct/sub-01_ses-01_task-Stroop_run-01_bold_valid_volreg.nii.gz | |
| 200301-22:11:41,624 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT1w.SpatialNormalization.SpatialNormalization". | |
| 2020-03-01 22:11:41,624 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT1w.SpatialNormalization.SpatialNormalization". | |
| 200301-22:11:41,940 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.funcMRIQC.ComputeIQMs.smoothness" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/funcMRIQC/ComputeIQMs/_in_file_..data..sub-01..ses-01..func..sub-01_ses-01_task-Stroop_run-01_bold.nii.gz/smoothness". | |
| 2020-03-01 22:11:41,940 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.funcMRIQC.ComputeIQMs.smoothness" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/funcMRIQC/ComputeIQMs/_in_file_..data..sub-01..ses-01..func..sub-01_ses-01_task-Stroop_run-01_bold.nii.gz/smoothness". | |
| 200301-22:11:41,943 nipype.workflow INFO: | |
| [Node] Running "smoothness" ("nipype.interfaces.afni.utils.FWHMx"), a CommandLine Interface with command: | |
| 3dFWHMx -ShowMeClassicFWHM -combine -detrend -input /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/funcMRIQC/_in_file_..data..sub-01..ses-01..func..sub-01_ses-01_task-Stroop_run-01_bold.nii.gz/mean/sub-01_ses-01_task-Stroop_run-01_bold_valid_volreg_tstat.nii.gz -mask /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..data..sub-01..ses-01..func..sub-01_ses-01_task-Stroop_run-01_bold.nii.gz/erode/sub-01_ses-01_task-Stroop_run-01_bold_valid_volreg_tstat_brain_mask_ero.nii.gz -detprefix sub-01_ses-01_task-Stroop_run-01_bold_valid_volreg_tstat_detrend -out sub-01_ses-01_task-Stroop_run-01_bold_valid_volreg_tstat_subbricks.out > sub-01_ses-01_task-Stroop_run-01_bold_valid_volreg_tstat_fwhmx.out | |
| 2020-03-01 22:11:41,943 nipype.workflow:INFO [Node] Running "smoothness" ("nipype.interfaces.afni.utils.FWHMx"), a CommandLine Interface with command: | |
| 3dFWHMx -ShowMeClassicFWHM -combine -detrend -input /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/funcMRIQC/_in_file_..data..sub-01..ses-01..func..sub-01_ses-01_task-Stroop_run-01_bold.nii.gz/mean/sub-01_ses-01_task-Stroop_run-01_bold_valid_volreg_tstat.nii.gz -mask /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..data..sub-01..ses-01..func..sub-01_ses-01_task-Stroop_run-01_bold.nii.gz/erode/sub-01_ses-01_task-Stroop_run-01_bold_valid_volreg_tstat_brain_mask_ero.nii.gz -detprefix sub-01_ses-01_task-Stroop_run-01_bold_valid_volreg_tstat_detrend -out sub-01_ses-01_task-Stroop_run-01_bold_valid_volreg_tstat_subbricks.out > sub-01_ses-01_task-Stroop_run-01_bold_valid_volreg_tstat_fwhmx.out | |
| 200301-22:11:43,754 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.funcMRIQC.ComputeIQMs.smoothness". | |
| 2020-03-01 22:11:43,754 nipype.workflow:INFO [Node] Finished "workflow_enumerator.funcMRIQC.ComputeIQMs.smoothness". | |
| 200301-22:11:43,953 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.funcMRIQC.ComputeIQMs.ComputeDVARS" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/funcMRIQC/ComputeIQMs/_in_file_..data..sub-01..ses-01..func..sub-01_ses-01_task-Stroop_run-01_bold.nii.gz/ComputeDVARS". | |
| 2020-03-01 22:11:43,953 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.funcMRIQC.ComputeIQMs.ComputeDVARS" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/funcMRIQC/ComputeIQMs/_in_file_..data..sub-01..ses-01..func..sub-01_ses-01_task-Stroop_run-01_bold.nii.gz/ComputeDVARS". | |
| 200301-22:11:43,955 nipype.workflow INFO: | |
| [Node] Running "ComputeDVARS" ("nipype.algorithms.confounds.ComputeDVARS") | |
| 2020-03-01 22:11:43,955 nipype.workflow:INFO [Node] Running "ComputeDVARS" ("nipype.algorithms.confounds.ComputeDVARS") | |
| 200301-22:11:48,439 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.funcMRIQC.ComputeIQMs.outliers". | |
| 2020-03-01 22:11:48,439 nipype.workflow:INFO [Node] Finished "workflow_enumerator.funcMRIQC.ComputeIQMs.outliers". | |
| 200301-22:11:49,934 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.funcMRIQC.SpatialNormalization.EPI2MNI" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/funcMRIQC/SpatialNormalization/_in_file_..data..sub-01..ses-01..func..sub-01_ses-01_task-Stroop_run-01_bold.nii.gz/EPI2MNI". | |
| 2020-03-01 22:11:49,934 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.funcMRIQC.SpatialNormalization.EPI2MNI" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/funcMRIQC/SpatialNormalization/_in_file_..data..sub-01..ses-01..func..sub-01_ses-01_task-Stroop_run-01_bold.nii.gz/EPI2MNI". | |
| 200301-22:11:49,937 nipype.workflow INFO: | |
| [Node] Running "EPI2MNI" ("niworkflows.interfaces.registration.RobustMNINormalizationRPT") | |
| 2020-03-01 22:11:49,937 nipype.workflow:INFO [Node] Running "EPI2MNI" ("niworkflows.interfaces.registration.RobustMNINormalizationRPT") | |
| 2020-03-01 22:11:49,938 niworkflows:INFO Estimating initial transform using AffineInitializer | |
| 200301-22:11:57,362 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.funcMRIQC.ComputeIQMs.gcor". | |
| 2020-03-01 22:11:57,362 nipype.workflow:INFO [Node] Finished "workflow_enumerator.funcMRIQC.ComputeIQMs.gcor". | |
| 200301-22:11:57,951 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.funcMRIQC.fMRI_HMC_afni.ComputeFD" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/funcMRIQC/fMRI_HMC_afni/_in_file_..data..sub-01..ses-01..func..sub-01_ses-01_task-Stroop_run-01_bold.nii.gz/ComputeFD". | |
| 2020-03-01 22:11:57,951 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.funcMRIQC.fMRI_HMC_afni.ComputeFD" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/funcMRIQC/fMRI_HMC_afni/_in_file_..data..sub-01..ses-01..func..sub-01_ses-01_task-Stroop_run-01_bold.nii.gz/ComputeFD". | |
| 200301-22:11:57,954 nipype.workflow INFO: | |
| [Node] Running "ComputeFD" ("nipype.algorithms.confounds.FramewiseDisplacement") | |
| 2020-03-01 22:11:57,954 nipype.workflow:INFO [Node] Running "ComputeFD" ("nipype.algorithms.confounds.FramewiseDisplacement") | |
| 200301-22:11:57,999 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.funcMRIQC.fMRI_HMC_afni.ComputeFD". | |
| 2020-03-01 22:11:57,999 nipype.workflow:INFO [Node] Finished "workflow_enumerator.funcMRIQC.fMRI_HMC_afni.ComputeFD". | |
| 200301-22:11:59,953 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.ComputeIQMs.harmonize" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT1w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/harmonize". | |
| 2020-03-01 22:11:59,953 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.ComputeIQMs.harmonize" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT1w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/harmonize". | |
| 200301-22:11:59,955 nipype.workflow INFO: | |
| [Node] Running "harmonize" ("mriqc.interfaces.anatomical.Harmonize") | |
| 2020-03-01 22:11:59,955 nipype.workflow:INFO [Node] Running "harmonize" ("mriqc.interfaces.anatomical.Harmonize") | |
| 200301-22:12:08,702 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT1w.ComputeIQMs.harmonize". | |
| 2020-03-01 22:12:08,702 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT1w.ComputeIQMs.harmonize". | |
| 200301-22:12:09,961 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.AirMaskWorkflow.invert_xfm" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT1w/AirMaskWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/invert_xfm". | |
| 2020-03-01 22:12:09,961 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.AirMaskWorkflow.invert_xfm" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT1w/AirMaskWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/invert_xfm". | |
| 200301-22:12:09,964 nipype.workflow INFO: | |
| [Node] Running "invert_xfm" ("nipype.interfaces.ants.resampling.ApplyTransforms"), a CommandLine Interface with command: | |
| antsApplyTransforms --default-value 0 --dimensionality 3 --float 1 --input /opt/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-01_desc-head_mask.nii.gz --interpolation MultiLabel --output tpl-MNI152NLin2009cAsym_res-01_desc-head_mask_trans.nii.gz --reference-image /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT1w/AFNISkullStripWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/binarize/sub-01_ses-01_T1w_conformed_calc_thresh.nii.gz --transform /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT1w/SpatialNormalization/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/SpatialNormalization/ants_t1_to_mniInverseComposite.h5 | |
| 2020-03-01 22:12:09,964 nipype.workflow:INFO [Node] Running "invert_xfm" ("nipype.interfaces.ants.resampling.ApplyTransforms"), a CommandLine Interface with command: | |
| antsApplyTransforms --default-value 0 --dimensionality 3 --float 1 --input /opt/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-01_desc-head_mask.nii.gz --interpolation MultiLabel --output tpl-MNI152NLin2009cAsym_res-01_desc-head_mask_trans.nii.gz --reference-image /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT1w/AFNISkullStripWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/binarize/sub-01_ses-01_T1w_conformed_calc_thresh.nii.gz --transform /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT1w/SpatialNormalization/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/SpatialNormalization/ants_t1_to_mniInverseComposite.h5 | |
| 200301-22:12:35,275 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.funcMRIQC.ComputeIQMs.ComputeDVARS". | |
| 2020-03-01 22:12:35,275 nipype.workflow:INFO [Node] Finished "workflow_enumerator.funcMRIQC.ComputeIQMs.ComputeDVARS". | |
| 200301-22:12:35,988 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.funcMRIQC.ComputeIQMs.measures" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/funcMRIQC/ComputeIQMs/_in_file_..data..sub-01..ses-01..func..sub-01_ses-01_task-Stroop_run-01_bold.nii.gz/measures". | |
| 2020-03-01 22:12:35,988 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.funcMRIQC.ComputeIQMs.measures" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/funcMRIQC/ComputeIQMs/_in_file_..data..sub-01..ses-01..func..sub-01_ses-01_task-Stroop_run-01_bold.nii.gz/measures". | |
| 200301-22:12:35,990 nipype.workflow INFO: | |
| [Node] Running "measures" ("mriqc.interfaces.functional.FunctionalQC") | |
| 2020-03-01 22:12:35,990 nipype.workflow:INFO [Node] Running "measures" ("mriqc.interfaces.functional.FunctionalQC") | |
| 200301-22:12:45,753 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.funcMRIQC.ComputeIQMs.measures". | |
| 2020-03-01 22:12:45,753 nipype.workflow:INFO [Node] Finished "workflow_enumerator.funcMRIQC.ComputeIQMs.measures". | |
| 200301-22:12:46,178 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.AFNISkullStripWorkflow.skullstrip" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT2w/AFNISkullStripWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/skullstrip". | |
| 2020-03-01 22:12:46,178 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.AFNISkullStripWorkflow.skullstrip" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT2w/AFNISkullStripWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/skullstrip". | |
| 200301-22:12:46,181 nipype.workflow INFO: | |
| [Node] Running "skullstrip" ("nipype.interfaces.afni.preprocess.SkullStrip"), a CommandLine Interface with command: | |
| 3dSkullStrip -input /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT2w/AFNISkullStripWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/skullstrip/sub-01_ses-01_T2w_conformed_corrected.nii.gz -prefix sub-01_ses-01_T2w_conformed_corrected_skullstrip.nii.gz | |
| 2020-03-01 22:12:46,181 nipype.workflow:INFO [Node] Running "skullstrip" ("nipype.interfaces.afni.preprocess.SkullStrip"), a CommandLine Interface with command: | |
| 3dSkullStrip -input /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT2w/AFNISkullStripWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/skullstrip/sub-01_ses-01_T2w_conformed_corrected.nii.gz -prefix sub-01_ses-01_T2w_conformed_corrected_skullstrip.nii.gz | |
| 2020-03-01 22:13:19,115 niworkflows:INFO Terminal outputs of initialization saved (/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/funcMRIQC/SpatialNormalization/_in_file_..data..sub-01..ses-01..func..sub-01_ses-01_task-Stroop_run-01_bold.nii.gz/EPI2MNI/stderr.nipype-init). | |
| 2020-03-01 22:13:19,116 niworkflows:INFO Loading settings from file /usr/local/miniconda/lib/python3.7/site-packages/niworkflows/data/bold-mni_registration_precise_000.json. | |
| 2020-03-01 22:13:19,118 niworkflows:INFO Retry #1, commandline: | |
| antsRegistration --collapse-output-transforms 1 --dimensionality 3 --float 0 --initial-moving-transform [ /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/funcMRIQC/SpatialNormalization/_in_file_..data..sub-01..ses-01..func..sub-01_ses-01_task-Stroop_run-01_bold.nii.gz/EPI2MNI/transform.mat, 0 ] --initialize-transforms-per-stage 0 --interpolation LanczosWindowedSinc --output [ epi_to_mni, epi_to_mni_Warped.nii.gz ] --transform Rigid[ 0.05 ] --metric Mattes[ /opt/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz, /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/funcMRIQC/SpatialNormalization/_in_file_..data..sub-01..ses-01..func..sub-01_ses-01_task-Stroop_run-01_bold.nii.gz/SharpenEPI/sub-01_ses-01_task-Stroop_run-01_bold_valid_volreg_tstat_corrected.nii.gz, 1, 56, Regular, 0.25 ] --convergence [ 10000x1000x100, 1e-06, 20 ] --smoothing-sigmas 4.0x2.0x1.0vox --shrink-factors 4x2x1 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --masks [ /opt/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz, /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..data..sub-01..ses-01..func..sub-01_ses-01_task-Stroop_run-01_bold.nii.gz/erode/sub-01_ses-01_task-Stroop_run-01_bold_valid_volreg_tstat_brain_mask_ero.nii.gz ] --transform Affine[ 0.08 ] --metric Mattes[ /opt/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz, /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/funcMRIQC/SpatialNormalization/_in_file_..data..sub-01..ses-01..func..sub-01_ses-01_task-Stroop_run-01_bold.nii.gz/SharpenEPI/sub-01_ses-01_task-Stroop_run-01_bold_valid_volreg_tstat_corrected.nii.gz, 1, 56, Regular, 0.25 ] --convergence [ 500x250x100, 1e-06, 20 ] --smoothing-sigmas 4.0x2.0x1.0vox --shrink-factors 8x4x2 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --masks [ /opt/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz, /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..data..sub-01..ses-01..func..sub-01_ses-01_task-Stroop_run-01_bold.nii.gz/erode/sub-01_ses-01_task-Stroop_run-01_bold_valid_volreg_tstat_brain_mask_ero.nii.gz ] --transform SyN[ 0.1, 3.0, 0.0 ] --metric CC[ /opt/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz, /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/funcMRIQC/SpatialNormalization/_in_file_..data..sub-01..ses-01..func..sub-01_ses-01_task-Stroop_run-01_bold.nii.gz/SharpenEPI/sub-01_ses-01_task-Stroop_run-01_bold_valid_volreg_tstat_corrected.nii.gz, 1, 4, None, 1 ] --convergence [ 100x30x20, 1e-06, 10 ] --smoothing-sigmas 3.0x2.0x1.0vox --shrink-factors 8x4x2 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --masks [ /opt/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz, /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/funcMRIQC/fMRIBrainMask/_in_file_..data..sub-01..ses-01..func..sub-01_ses-01_task-Stroop_run-01_bold.nii.gz/erode/sub-01_ses-01_task-Stroop_run-01_bold_valid_volreg_tstat_brain_mask_ero.nii.gz ] --winsorize-image-intensities [ 0.005, 0.995 ] --write-composite-transform 1 | |
| 200301-22:15:27,921 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT2w.AFNISkullStripWorkflow.skullstrip". | |
| 2020-03-01 22:15:27,921 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT2w.AFNISkullStripWorkflow.skullstrip". | |
| 200301-22:15:28,149 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.funcMRIQC.UploadMetrics" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/funcMRIQC/_in_file_..data..sub-01..ses-01..func..sub-01_ses-01_task-Stroop_run-01_bold.nii.gz/UploadMetrics". | |
| 2020-03-01 22:15:28,149 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.funcMRIQC.UploadMetrics" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/funcMRIQC/_in_file_..data..sub-01..ses-01..func..sub-01_ses-01_task-Stroop_run-01_bold.nii.gz/UploadMetrics". | |
| 200301-22:15:28,151 nipype.workflow INFO: | |
| [Node] Running "UploadMetrics" ("mriqc.interfaces.webapi.UploadIQMs") | |
| 2020-03-01 22:15:28,151 nipype.workflow:INFO [Node] Running "UploadMetrics" ("mriqc.interfaces.webapi.UploadIQMs") | |
| 200301-22:15:29,657 nipype.interface INFO: | |
| MRIQC Web API: submitting to <https://mriqc.nimh.nih.gov:443/api/v1/bold> | |
| 2020-03-01 22:15:29,657 nipype.interface:INFO MRIQC Web API: submitting to <https://mriqc.nimh.nih.gov:443/api/v1/bold> | |
| 200301-22:15:30,206 nipype.interface INFO: | |
| QC metrics successfully uploaded. | |
| 2020-03-01 22:15:30,206 nipype.interface:INFO QC metrics successfully uploaded. | |
| 200301-22:15:30,209 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.funcMRIQC.UploadMetrics". | |
| 2020-03-01 22:15:30,209 nipype.workflow:INFO [Node] Finished "workflow_enumerator.funcMRIQC.UploadMetrics". | |
| 200301-22:15:32,150 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.AFNISkullStripWorkflow.sstrip_orig_vol" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT2w/AFNISkullStripWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/sstrip_orig_vol". | |
| 2020-03-01 22:15:32,150 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.AFNISkullStripWorkflow.sstrip_orig_vol" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT2w/AFNISkullStripWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/sstrip_orig_vol". | |
| 200301-22:15:32,152 nipype.workflow INFO: | |
| [Node] Running "sstrip_orig_vol" ("nipype.interfaces.afni.utils.Calc"), a CommandLine Interface with command: | |
| 3dcalc -a /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT2w/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/conform/sub-01_ses-01_T2w_conformed.nii.gz -b /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT2w/AFNISkullStripWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/skullstrip/sub-01_ses-01_T2w_conformed_corrected_skullstrip.nii.gz -expr "a*step(b)" -prefix sub-01_ses-01_T2w_conformed_calc.nii.gz | |
| 2020-03-01 22:15:32,152 nipype.workflow:INFO [Node] Running "sstrip_orig_vol" ("nipype.interfaces.afni.utils.Calc"), a CommandLine Interface with command: | |
| 3dcalc -a /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT2w/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/conform/sub-01_ses-01_T2w_conformed.nii.gz -b /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT2w/AFNISkullStripWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/skullstrip/sub-01_ses-01_T2w_conformed_corrected_skullstrip.nii.gz -expr "a*step(b)" -prefix sub-01_ses-01_T2w_conformed_calc.nii.gz | |
| 200301-22:15:36,245 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT2w.AFNISkullStripWorkflow.sstrip_orig_vol". | |
| 2020-03-01 22:15:36,245 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT2w.AFNISkullStripWorkflow.sstrip_orig_vol". | |
| 200301-22:15:38,152 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.segmentation" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT2w/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/segmentation". | |
| 2020-03-01 22:15:38,152 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.segmentation" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT2w/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/segmentation". | |
| 200301-22:15:38,156 nipype.workflow INFO: | |
| [Node] Running "segmentation" ("nipype.interfaces.fsl.preprocess.FAST"), a CommandLine Interface with command: | |
| fast -t 2 -o segment -g -S 1 /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT2w/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/segmentation/sub-01_ses-01_T2w_conformed_calc.nii.gz | |
| 2020-03-01 22:15:38,156 nipype.workflow:INFO [Node] Running "segmentation" ("nipype.interfaces.fsl.preprocess.FAST"), a CommandLine Interface with command: | |
| fast -t 2 -o segment -g -S 1 /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT2w/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/segmentation/sub-01_ses-01_T2w_conformed_calc.nii.gz | |
| 2020-03-01 22:16:18,634 niworkflows:INFO Successful spatial normalization (retry #1). | |
| 2020-03-01 22:16:18,635 niworkflows:INFO Report - setting fixed (/opt/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz) and moving (/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/funcMRIQC/SpatialNormalization/_in_file_..data..sub-01..ses-01..func..sub-01_ses-01_task-Stroop_run-01_bold.nii.gz/EPI2MNI/epi_to_mni_Warped.nii.gz) images | |
| 2020-03-01 22:16:18,635 niworkflows:INFO Generating visual report | |
| 200301-22:16:31,728 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.funcMRIQC.SpatialNormalization.EPI2MNI". | |
| 2020-03-01 22:16:31,728 nipype.workflow:INFO [Node] Finished "workflow_enumerator.funcMRIQC.SpatialNormalization.EPI2MNI". | |
| 200301-22:16:32,218 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.funcMRIQC.SpatialNormalization.ResampleSegmentation" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/funcMRIQC/SpatialNormalization/_in_file_..data..sub-01..ses-01..func..sub-01_ses-01_task-Stroop_run-01_bold.nii.gz/ResampleSegmentation". | |
| 2020-03-01 22:16:32,218 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.funcMRIQC.SpatialNormalization.ResampleSegmentation" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/funcMRIQC/SpatialNormalization/_in_file_..data..sub-01..ses-01..func..sub-01_ses-01_task-Stroop_run-01_bold.nii.gz/ResampleSegmentation". | |
| 200301-22:16:32,221 nipype.workflow INFO: | |
| [Node] Running "ResampleSegmentation" ("nipype.interfaces.ants.resampling.ApplyTransforms"), a CommandLine Interface with command: | |
| antsApplyTransforms --default-value 0 --dimensionality 3 --float 1 --input /opt/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-01_desc-carpet_dseg.nii.gz --interpolation MultiLabel --output tpl-MNI152NLin2009cAsym_res-01_desc-carpet_dseg_trans.nii.gz --reference-image /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/funcMRIQC/_in_file_..data..sub-01..ses-01..func..sub-01_ses-01_task-Stroop_run-01_bold.nii.gz/mean/sub-01_ses-01_task-Stroop_run-01_bold_valid_volreg_tstat.nii.gz --transform /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/funcMRIQC/SpatialNormalization/_in_file_..data..sub-01..ses-01..func..sub-01_ses-01_task-Stroop_run-01_bold.nii.gz/EPI2MNI/epi_to_mniInverseComposite.h5 | |
| 2020-03-01 22:16:32,221 nipype.workflow:INFO [Node] Running "ResampleSegmentation" ("nipype.interfaces.ants.resampling.ApplyTransforms"), a CommandLine Interface with command: | |
| antsApplyTransforms --default-value 0 --dimensionality 3 --float 1 --input /opt/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-01_desc-carpet_dseg.nii.gz --interpolation MultiLabel --output tpl-MNI152NLin2009cAsym_res-01_desc-carpet_dseg_trans.nii.gz --reference-image /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/funcMRIQC/_in_file_..data..sub-01..ses-01..func..sub-01_ses-01_task-Stroop_run-01_bold.nii.gz/mean/sub-01_ses-01_task-Stroop_run-01_bold_valid_volreg_tstat.nii.gz --transform /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/funcMRIQC/SpatialNormalization/_in_file_..data..sub-01..ses-01..func..sub-01_ses-01_task-Stroop_run-01_bold.nii.gz/EPI2MNI/epi_to_mniInverseComposite.h5 | |
| 200301-22:16:43,257 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.funcMRIQC.SpatialNormalization.ResampleSegmentation". | |
| 2020-03-01 22:16:43,257 nipype.workflow:INFO [Node] Finished "workflow_enumerator.funcMRIQC.SpatialNormalization.ResampleSegmentation". | |
| 200301-22:16:44,232 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.funcMRIQC.ReportsWorkflow.BigPlot" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/funcMRIQC/ReportsWorkflow/_in_file_..data..sub-01..ses-01..func..sub-01_ses-01_task-Stroop_run-01_bold.nii.gz/BigPlot". | |
| 2020-03-01 22:16:44,232 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.funcMRIQC.ReportsWorkflow.BigPlot" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/funcMRIQC/ReportsWorkflow/_in_file_..data..sub-01..ses-01..func..sub-01_ses-01_task-Stroop_run-01_bold.nii.gz/BigPlot". | |
| 200301-22:16:44,235 nipype.workflow INFO: | |
| [Node] Running "BigPlot" ("niworkflows.interfaces.plotting.FMRISummary") | |
| 2020-03-01 22:16:44,235 nipype.workflow:INFO [Node] Running "BigPlot" ("niworkflows.interfaces.plotting.FMRISummary") | |
| 200301-22:17:06,222 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.funcMRIQC.ReportsWorkflow.BigPlot". | |
| 2020-03-01 22:17:06,222 nipype.workflow:INFO [Node] Finished "workflow_enumerator.funcMRIQC.ReportsWorkflow.BigPlot". | |
| 200301-22:17:08,251 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.funcMRIQC.ReportsWorkflow.MergePlots" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/funcMRIQC/ReportsWorkflow/_in_file_..data..sub-01..ses-01..func..sub-01_ses-01_task-Stroop_run-01_bold.nii.gz/MergePlots". | |
| 2020-03-01 22:17:08,251 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.funcMRIQC.ReportsWorkflow.MergePlots" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/funcMRIQC/ReportsWorkflow/_in_file_..data..sub-01..ses-01..func..sub-01_ses-01_task-Stroop_run-01_bold.nii.gz/MergePlots". | |
| 200301-22:17:08,254 nipype.workflow INFO: | |
| [Node] Running "MergePlots" ("nipype.interfaces.utility.base.Merge") | |
| 2020-03-01 22:17:08,254 nipype.workflow:INFO [Node] Running "MergePlots" ("nipype.interfaces.utility.base.Merge") | |
| 200301-22:17:08,258 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.funcMRIQC.ReportsWorkflow.MergePlots". | |
| 2020-03-01 22:17:08,258 nipype.workflow:INFO [Node] Finished "workflow_enumerator.funcMRIQC.ReportsWorkflow.MergePlots". | |
| 200301-22:17:10,265 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.funcMRIQC.ReportsWorkflow.GenerateReport" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/funcMRIQC/ReportsWorkflow/_in_file_..data..sub-01..ses-01..func..sub-01_ses-01_task-Stroop_run-01_bold.nii.gz/GenerateReport". | |
| 2020-03-01 22:17:10,265 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.funcMRIQC.ReportsWorkflow.GenerateReport" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/funcMRIQC/ReportsWorkflow/_in_file_..data..sub-01..ses-01..func..sub-01_ses-01_task-Stroop_run-01_bold.nii.gz/GenerateReport". | |
| 200301-22:17:10,267 nipype.workflow INFO: | |
| [Node] Running "GenerateReport" ("nipype.interfaces.utility.wrappers.Function") | |
| 2020-03-01 22:17:10,267 nipype.workflow:INFO [Node] Running "GenerateReport" ("nipype.interfaces.utility.wrappers.Function") | |
| 2020-03-01 22:17:10,498 mriqc.report:WARNING Building bold report: no exclude index was found | |
| 200301-22:17:10,626 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.funcMRIQC.ReportsWorkflow.GenerateReport". | |
| 2020-03-01 22:17:10,626 nipype.workflow:INFO [Node] Finished "workflow_enumerator.funcMRIQC.ReportsWorkflow.GenerateReport". | |
| 200301-22:17:12,471 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.AFNISkullStripWorkflow.binarize" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT2w/AFNISkullStripWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/binarize". | |
| 2020-03-01 22:17:12,471 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.AFNISkullStripWorkflow.binarize" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT2w/AFNISkullStripWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/binarize". | |
| 200301-22:17:12,473 nipype.workflow INFO: | |
| [Node] Running "binarize" ("nipype.interfaces.fsl.maths.Threshold"), a CommandLine Interface with command: | |
| fslmaths /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT2w/AFNISkullStripWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/sstrip_orig_vol/sub-01_ses-01_T2w_conformed_calc.nii.gz -thr 0.0010000000 -bin /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT2w/AFNISkullStripWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/binarize/sub-01_ses-01_T2w_conformed_calc_thresh.nii.gz | |
| 2020-03-01 22:17:12,473 nipype.workflow:INFO [Node] Running "binarize" ("nipype.interfaces.fsl.maths.Threshold"), a CommandLine Interface with command: | |
| fslmaths /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT2w/AFNISkullStripWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/sstrip_orig_vol/sub-01_ses-01_T2w_conformed_calc.nii.gz -thr 0.0010000000 -bin /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT2w/AFNISkullStripWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/binarize/sub-01_ses-01_T2w_conformed_calc_thresh.nii.gz | |
| 200301-22:17:15,330 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT2w.AFNISkullStripWorkflow.binarize". | |
| 2020-03-01 22:17:15,330 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT2w.AFNISkullStripWorkflow.binarize". | |
| 200301-22:17:16,265 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.ReportsWorkflow.PlotMosaicZoomed" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT2w/ReportsWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/PlotMosaicZoomed". | |
| 2020-03-01 22:17:16,265 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.ReportsWorkflow.PlotMosaicZoomed" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT2w/ReportsWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/PlotMosaicZoomed". | |
| 200301-22:17:16,267 nipype.workflow INFO: | |
| [Node] Running "PlotMosaicZoomed" ("mriqc.interfaces.viz.PlotMosaic") | |
| 2020-03-01 22:17:16,267 nipype.workflow:INFO [Node] Running "PlotMosaicZoomed" ("mriqc.interfaces.viz.PlotMosaic") | |
| 200301-22:17:40,48 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT2w.ReportsWorkflow.PlotMosaicZoomed". | |
| 2020-03-01 22:17:40,048 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT2w.ReportsWorkflow.PlotMosaicZoomed". | |
| 200301-22:17:40,278 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.ReportsWorkflow.MergePlots" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT2w/ReportsWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/MergePlots". | |
| 2020-03-01 22:17:40,278 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.ReportsWorkflow.MergePlots" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT2w/ReportsWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/MergePlots". | |
| 200301-22:17:40,280 nipype.workflow INFO: | |
| [Node] Running "MergePlots" ("nipype.interfaces.utility.base.Merge") | |
| 2020-03-01 22:17:40,280 nipype.workflow:INFO [Node] Running "MergePlots" ("nipype.interfaces.utility.base.Merge") | |
| 200301-22:17:40,283 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT2w.ReportsWorkflow.MergePlots". | |
| 2020-03-01 22:17:40,283 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT2w.ReportsWorkflow.MergePlots". | |
| 200301-22:17:42,272 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.ComputeIQMs.smoothness" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT2w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/smoothness". | |
| 2020-03-01 22:17:42,272 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.ComputeIQMs.smoothness" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT2w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/smoothness". | |
| 200301-22:17:42,275 nipype.workflow INFO: | |
| [Node] Running "smoothness" ("nipype.interfaces.afni.utils.FWHMx"), a CommandLine Interface with command: | |
| 3dFWHMx -ShowMeClassicFWHM -combine -detrend -input /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT2w/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/conform/sub-01_ses-01_T2w_conformed.nii.gz -mask /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT2w/AFNISkullStripWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/binarize/sub-01_ses-01_T2w_conformed_calc_thresh.nii.gz -detprefix sub-01_ses-01_T2w_conformed_detrend -out sub-01_ses-01_T2w_conformed_subbricks.out > sub-01_ses-01_T2w_conformed_fwhmx.out | |
| 2020-03-01 22:17:42,275 nipype.workflow:INFO [Node] Running "smoothness" ("nipype.interfaces.afni.utils.FWHMx"), a CommandLine Interface with command: | |
| 3dFWHMx -ShowMeClassicFWHM -combine -detrend -input /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT2w/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/conform/sub-01_ses-01_T2w_conformed.nii.gz -mask /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT2w/AFNISkullStripWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/binarize/sub-01_ses-01_T2w_conformed_calc_thresh.nii.gz -detprefix sub-01_ses-01_T2w_conformed_detrend -out sub-01_ses-01_T2w_conformed_subbricks.out > sub-01_ses-01_T2w_conformed_fwhmx.out | |
| 200301-22:17:43,834 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT1w.AirMaskWorkflow.invert_xfm". | |
| 2020-03-01 22:17:43,834 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT1w.AirMaskWorkflow.invert_xfm". | |
| 200301-22:17:44,299 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.AirMaskWorkflow.ArtifactMask" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT1w/AirMaskWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/ArtifactMask". | |
| 2020-03-01 22:17:44,299 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.AirMaskWorkflow.ArtifactMask" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT1w/AirMaskWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/ArtifactMask". | |
| 200301-22:17:44,302 nipype.workflow INFO: | |
| [Node] Running "ArtifactMask" ("mriqc.interfaces.anatomical.ArtifactMask") | |
| 2020-03-01 22:17:44,302 nipype.workflow:INFO [Node] Running "ArtifactMask" ("mriqc.interfaces.anatomical.ArtifactMask") | |
| 200301-22:17:57,318 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT1w.AirMaskWorkflow.ArtifactMask". | |
| 2020-03-01 22:17:57,318 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT1w.AirMaskWorkflow.ArtifactMask". | |
| 200301-22:17:58,308 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.ComputeIQMs.ComputeQI2" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT1w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/ComputeQI2". | |
| 2020-03-01 22:17:58,308 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.ComputeIQMs.ComputeQI2" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT1w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/ComputeQI2". | |
| 200301-22:17:58,310 nipype.workflow INFO: | |
| [Node] Running "ComputeQI2" ("mriqc.interfaces.anatomical.ComputeQI2") | |
| 2020-03-01 22:17:58,310 nipype.workflow:INFO [Node] Running "ComputeQI2" ("mriqc.interfaces.anatomical.ComputeQI2") | |
| 200301-22:18:01,807 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT2w.ComputeIQMs.smoothness". | |
| 2020-03-01 22:18:01,807 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT2w.ComputeIQMs.smoothness". | |
| 200301-22:18:02,315 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.ComputeIQMs.provenance" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT1w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/provenance". | |
| 2020-03-01 22:18:02,315 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.ComputeIQMs.provenance" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT1w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/provenance". | |
| 200301-22:18:02,318 nipype.workflow INFO: | |
| [Node] Running "provenance" ("nipype.interfaces.utility.wrappers.Function") | |
| 2020-03-01 22:18:02,318 nipype.workflow:INFO [Node] Running "provenance" ("nipype.interfaces.utility.wrappers.Function") | |
| 200301-22:18:02,696 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT1w.ComputeIQMs.provenance". | |
| 2020-03-01 22:18:02,696 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT1w.ComputeIQMs.provenance". | |
| 200301-22:18:04,309 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.SpatialNormalization.SpatialNormalization" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT2w/SpatialNormalization/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/SpatialNormalization". | |
| 2020-03-01 22:18:04,309 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.SpatialNormalization.SpatialNormalization" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT2w/SpatialNormalization/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/SpatialNormalization". | |
| 200301-22:18:04,311 nipype.workflow INFO: | |
| [Node] Running "SpatialNormalization" ("niworkflows.interfaces.registration.RobustMNINormalizationRPT") | |
| 2020-03-01 22:18:04,311 nipype.workflow:INFO [Node] Running "SpatialNormalization" ("niworkflows.interfaces.registration.RobustMNINormalizationRPT") | |
| 2020-03-01 22:18:07,685 niworkflows:INFO Estimating initial transform using AffineInitializer | |
| 200301-22:19:05,59 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT1w.ComputeIQMs.ComputeQI2". | |
| 2020-03-01 22:19:05,059 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT1w.ComputeIQMs.ComputeQI2". | |
| 200301-22:19:06,371 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.ComputeIQMs.metadata" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT2w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/metadata". | |
| 2020-03-01 22:19:06,371 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.ComputeIQMs.metadata" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT2w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/metadata". | |
| 200301-22:19:06,384 nipype.workflow INFO: | |
| [Node] Running "metadata" ("niworkflows.interfaces.bids.ReadSidecarJSON") | |
| 2020-03-01 22:19:06,384 nipype.workflow:INFO [Node] Running "metadata" ("niworkflows.interfaces.bids.ReadSidecarJSON") | |
| 200301-22:19:06,452 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT2w.ComputeIQMs.metadata". | |
| 2020-03-01 22:19:06,452 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT2w.ComputeIQMs.metadata". | |
| 200301-22:19:08,362 nipype.workflow INFO: | |
| [Node] Setting-up "_MNItpms2t10" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT1w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/MNItpms2t1/mapflow/_MNItpms2t10". | |
| 2020-03-01 22:19:08,362 nipype.workflow:INFO [Node] Setting-up "_MNItpms2t10" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT1w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/MNItpms2t1/mapflow/_MNItpms2t10". | |
| 200301-22:19:08,366 nipype.workflow INFO: | |
| [Node] Running "_MNItpms2t10" ("nipype.interfaces.ants.resampling.ApplyTransforms"), a CommandLine Interface with command: | |
| antsApplyTransforms --default-value 0 --dimensionality 3 --float 1 --input /opt/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-01_label-CSF_probseg.nii.gz --interpolation Linear --output tpl-MNI152NLin2009cAsym_res-01_label-CSF_probseg_trans.nii.gz --reference-image /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT1w/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/conform/sub-01_ses-01_T1w_conformed.nii.gz --transform /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT1w/SpatialNormalization/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/SpatialNormalization/ants_t1_to_mniInverseComposite.h5 | |
| 2020-03-01 22:19:08,366 nipype.workflow:INFO [Node] Running "_MNItpms2t10" ("nipype.interfaces.ants.resampling.ApplyTransforms"), a CommandLine Interface with command: | |
| antsApplyTransforms --default-value 0 --dimensionality 3 --float 1 --input /opt/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-01_label-CSF_probseg.nii.gz --interpolation Linear --output tpl-MNI152NLin2009cAsym_res-01_label-CSF_probseg_trans.nii.gz --reference-image /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT1w/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/conform/sub-01_ses-01_T1w_conformed.nii.gz --transform /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT1w/SpatialNormalization/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/SpatialNormalization/ants_t1_to_mniInverseComposite.h5 | |
| 200301-22:19:19,321 nipype.workflow INFO: | |
| [Node] Finished "_MNItpms2t10". | |
| 2020-03-01 22:19:19,321 nipype.workflow:INFO [Node] Finished "_MNItpms2t10". | |
| 200301-22:19:20,375 nipype.workflow INFO: | |
| [Node] Setting-up "_MNItpms2t11" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT1w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/MNItpms2t1/mapflow/_MNItpms2t11". | |
| 2020-03-01 22:19:20,375 nipype.workflow:INFO [Node] Setting-up "_MNItpms2t11" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT1w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/MNItpms2t1/mapflow/_MNItpms2t11". | |
| 200301-22:19:20,379 nipype.workflow INFO: | |
| [Node] Running "_MNItpms2t11" ("nipype.interfaces.ants.resampling.ApplyTransforms"), a CommandLine Interface with command: | |
| antsApplyTransforms --default-value 0 --dimensionality 3 --float 1 --input /opt/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-01_label-GM_probseg.nii.gz --interpolation Linear --output tpl-MNI152NLin2009cAsym_res-01_label-GM_probseg_trans.nii.gz --reference-image /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT1w/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/conform/sub-01_ses-01_T1w_conformed.nii.gz --transform /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT1w/SpatialNormalization/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/SpatialNormalization/ants_t1_to_mniInverseComposite.h5 | |
| 2020-03-01 22:19:20,379 nipype.workflow:INFO [Node] Running "_MNItpms2t11" ("nipype.interfaces.ants.resampling.ApplyTransforms"), a CommandLine Interface with command: | |
| antsApplyTransforms --default-value 0 --dimensionality 3 --float 1 --input /opt/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-01_label-GM_probseg.nii.gz --interpolation Linear --output tpl-MNI152NLin2009cAsym_res-01_label-GM_probseg_trans.nii.gz --reference-image /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT1w/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/conform/sub-01_ses-01_T1w_conformed.nii.gz --transform /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT1w/SpatialNormalization/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/SpatialNormalization/ants_t1_to_mniInverseComposite.h5 | |
| 200301-22:19:31,501 nipype.workflow INFO: | |
| [Node] Finished "_MNItpms2t11". | |
| 2020-03-01 22:19:31,501 nipype.workflow:INFO [Node] Finished "_MNItpms2t11". | |
| 200301-22:19:32,383 nipype.workflow INFO: | |
| [Node] Setting-up "_MNItpms2t12" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT1w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/MNItpms2t1/mapflow/_MNItpms2t12". | |
| 2020-03-01 22:19:32,383 nipype.workflow:INFO [Node] Setting-up "_MNItpms2t12" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT1w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/MNItpms2t1/mapflow/_MNItpms2t12". | |
| 200301-22:19:32,386 nipype.workflow INFO: | |
| [Node] Running "_MNItpms2t12" ("nipype.interfaces.ants.resampling.ApplyTransforms"), a CommandLine Interface with command: | |
| antsApplyTransforms --default-value 0 --dimensionality 3 --float 1 --input /opt/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-01_label-WM_probseg.nii.gz --interpolation Linear --output tpl-MNI152NLin2009cAsym_res-01_label-WM_probseg_trans.nii.gz --reference-image /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT1w/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/conform/sub-01_ses-01_T1w_conformed.nii.gz --transform /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT1w/SpatialNormalization/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/SpatialNormalization/ants_t1_to_mniInverseComposite.h5 | |
| 2020-03-01 22:19:32,386 nipype.workflow:INFO [Node] Running "_MNItpms2t12" ("nipype.interfaces.ants.resampling.ApplyTransforms"), a CommandLine Interface with command: | |
| antsApplyTransforms --default-value 0 --dimensionality 3 --float 1 --input /opt/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-01_label-WM_probseg.nii.gz --interpolation Linear --output tpl-MNI152NLin2009cAsym_res-01_label-WM_probseg_trans.nii.gz --reference-image /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT1w/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/conform/sub-01_ses-01_T1w_conformed.nii.gz --transform /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT1w/SpatialNormalization/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/SpatialNormalization/ants_t1_to_mniInverseComposite.h5 | |
| 200301-22:19:43,477 nipype.workflow INFO: | |
| [Node] Finished "_MNItpms2t12". | |
| 2020-03-01 22:19:43,477 nipype.workflow:INFO [Node] Finished "_MNItpms2t12". | |
| 200301-22:19:44,396 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.ComputeIQMs.MNItpms2t1" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT1w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/MNItpms2t1". | |
| 2020-03-01 22:19:44,396 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.ComputeIQMs.MNItpms2t1" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT1w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/MNItpms2t1". | |
| 200301-22:19:44,400 nipype.workflow INFO: | |
| [Node] Setting-up "_MNItpms2t10" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT1w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/MNItpms2t1/mapflow/_MNItpms2t10". | |
| 2020-03-01 22:19:44,400 nipype.workflow:INFO [Node] Setting-up "_MNItpms2t10" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT1w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/MNItpms2t1/mapflow/_MNItpms2t10". | |
| 200301-22:19:44,401 nipype.workflow INFO: | |
| [Node] Cached "_MNItpms2t10" - collecting precomputed outputs | |
| 2020-03-01 22:19:44,401 nipype.workflow:INFO [Node] Cached "_MNItpms2t10" - collecting precomputed outputs | |
| 200301-22:19:44,401 nipype.workflow INFO: | |
| [Node] "_MNItpms2t10" found cached. | |
| 2020-03-01 22:19:44,401 nipype.workflow:INFO [Node] "_MNItpms2t10" found cached. | |
| 200301-22:19:44,402 nipype.workflow INFO: | |
| [Node] Setting-up "_MNItpms2t11" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT1w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/MNItpms2t1/mapflow/_MNItpms2t11". | |
| 2020-03-01 22:19:44,402 nipype.workflow:INFO [Node] Setting-up "_MNItpms2t11" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT1w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/MNItpms2t1/mapflow/_MNItpms2t11". | |
| 200301-22:19:44,403 nipype.workflow INFO: | |
| [Node] Cached "_MNItpms2t11" - collecting precomputed outputs | |
| 2020-03-01 22:19:44,403 nipype.workflow:INFO [Node] Cached "_MNItpms2t11" - collecting precomputed outputs | |
| 200301-22:19:44,403 nipype.workflow INFO: | |
| [Node] "_MNItpms2t11" found cached. | |
| 2020-03-01 22:19:44,403 nipype.workflow:INFO [Node] "_MNItpms2t11" found cached. | |
| 200301-22:19:44,404 nipype.workflow INFO: | |
| [Node] Setting-up "_MNItpms2t12" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT1w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/MNItpms2t1/mapflow/_MNItpms2t12". | |
| 2020-03-01 22:19:44,404 nipype.workflow:INFO [Node] Setting-up "_MNItpms2t12" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT1w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/MNItpms2t1/mapflow/_MNItpms2t12". | |
| 200301-22:19:44,405 nipype.workflow INFO: | |
| [Node] Cached "_MNItpms2t12" - collecting precomputed outputs | |
| 2020-03-01 22:19:44,405 nipype.workflow:INFO [Node] Cached "_MNItpms2t12" - collecting precomputed outputs | |
| 200301-22:19:44,405 nipype.workflow INFO: | |
| [Node] "_MNItpms2t12" found cached. | |
| 2020-03-01 22:19:44,405 nipype.workflow:INFO [Node] "_MNItpms2t12" found cached. | |
| 200301-22:19:44,416 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT1w.ComputeIQMs.MNItpms2t1". | |
| 2020-03-01 22:19:44,416 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT1w.ComputeIQMs.MNItpms2t1". | |
| 200301-22:19:46,408 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.ComputeIQMs.measures" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT1w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/measures". | |
| 2020-03-01 22:19:46,408 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.ComputeIQMs.measures" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT1w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/measures". | |
| 200301-22:19:46,411 nipype.workflow INFO: | |
| [Node] Running "measures" ("mriqc.interfaces.anatomical.StructuralQC") | |
| 2020-03-01 22:19:46,411 nipype.workflow:INFO [Node] Running "measures" ("mriqc.interfaces.anatomical.StructuralQC") | |
| 200301-22:20:09,749 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT1w.ComputeIQMs.measures". | |
| 2020-03-01 22:20:09,749 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT1w.ComputeIQMs.measures". | |
| 200301-22:20:12,433 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.ReportsWorkflow.GenerateReport" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT1w/ReportsWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/GenerateReport". | |
| 2020-03-01 22:20:12,433 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.ReportsWorkflow.GenerateReport" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT1w/ReportsWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/GenerateReport". | |
| 200301-22:20:12,436 nipype.workflow INFO: | |
| [Node] Running "GenerateReport" ("nipype.interfaces.utility.wrappers.Function") | |
| 2020-03-01 22:20:12,436 nipype.workflow:INFO [Node] Running "GenerateReport" ("nipype.interfaces.utility.wrappers.Function") | |
| 200301-22:20:12,815 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT1w.ReportsWorkflow.GenerateReport". | |
| 2020-03-01 22:20:12,815 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT1w.ReportsWorkflow.GenerateReport". | |
| 200301-22:20:14,872 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.UploadMetrics" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT1w/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/UploadMetrics". | |
| 2020-03-01 22:20:14,872 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.UploadMetrics" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT1w/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/UploadMetrics". | |
| 200301-22:20:14,875 nipype.workflow INFO: | |
| [Node] Running "UploadMetrics" ("mriqc.interfaces.webapi.UploadIQMs") | |
| 2020-03-01 22:20:14,875 nipype.workflow:INFO [Node] Running "UploadMetrics" ("mriqc.interfaces.webapi.UploadIQMs") | |
| 200301-22:20:15,564 nipype.interface INFO: | |
| MRIQC Web API: submitting to <https://mriqc.nimh.nih.gov:443/api/v1/T1w> | |
| 2020-03-01 22:20:15,564 nipype.interface:INFO MRIQC Web API: submitting to <https://mriqc.nimh.nih.gov:443/api/v1/T1w> | |
| 200301-22:20:15,704 nipype.interface INFO: | |
| QC metrics successfully uploaded. | |
| 2020-03-01 22:20:15,704 nipype.interface:INFO QC metrics successfully uploaded. | |
| 200301-22:20:15,707 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT1w.UploadMetrics". | |
| 2020-03-01 22:20:15,707 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT1w.UploadMetrics". | |
| 2020-03-01 22:21:21,324 niworkflows:INFO Terminal outputs of initialization saved (/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT2w/SpatialNormalization/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/SpatialNormalization/stderr.nipype-init). | |
| 2020-03-01 22:21:21,324 niworkflows:INFO Loading settings from file /usr/local/miniconda/lib/python3.7/site-packages/niworkflows/data/t1w-mni_registration_fast_000.json. | |
| 2020-03-01 22:21:21,325 niworkflows:INFO Retry #1, commandline: | |
| antsRegistration --collapse-output-transforms 1 --dimensionality 3 --float 0 --initial-moving-transform [ /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT2w/SpatialNormalization/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/SpatialNormalization/transform.mat, 0 ] --initialize-transforms-per-stage 0 --interpolation LanczosWindowedSinc --output [ ants_t1_to_mni, ants_t1_to_mni_Warped.nii.gz ] --transform Rigid[ 0.01 ] --metric Mattes[ /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT2w/SpatialNormalization/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/SpatialNormalization/fixed_masked.nii.gz, /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT2w/SpatialNormalization/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/SpatialNormalization/moving_masked.nii.gz, 1, 32, Random, 0.15 ] --convergence [ 1000, 1e-06, 20 ] --smoothing-sigmas 4.0vox --shrink-factors 4 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --transform Affine[ 0.08 ] --metric Mattes[ /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT2w/SpatialNormalization/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/SpatialNormalization/fixed_masked.nii.gz, /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT2w/SpatialNormalization/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/SpatialNormalization/moving_masked.nii.gz, 1, 32, Regular, 0.15 ] --convergence [ 500x250x100, 1e-06, 20 ] --smoothing-sigmas 4.0x2.0x0.0vox --shrink-factors 4x2x1 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --transform SyN[ 0.1, 3.0, 0.0 ] --metric Mattes[ /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT2w/SpatialNormalization/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/SpatialNormalization/fixed_masked.nii.gz, /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT2w/SpatialNormalization/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/SpatialNormalization/moving_masked.nii.gz, 1, 56, Regular, 0.25 ] --convergence [ 50x20, 1e-06, 10 ] --smoothing-sigmas 1.0x0.0vox --shrink-factors 2x1 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --winsorize-image-intensities [ 0.0, 1.0 ] --write-composite-transform 1 | |
| 200301-22:23:50,56 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT2w.segmentation". | |
| 2020-03-01 22:23:50,056 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT2w.segmentation". | |
| 200301-22:23:50,465 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.ComputeIQMs.harmonize" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT2w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/harmonize". | |
| 2020-03-01 22:23:50,465 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.ComputeIQMs.harmonize" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT2w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/harmonize". | |
| 200301-22:23:50,468 nipype.workflow INFO: | |
| [Node] Running "harmonize" ("mriqc.interfaces.anatomical.Harmonize") | |
| 2020-03-01 22:23:50,468 nipype.workflow:INFO [Node] Running "harmonize" ("mriqc.interfaces.anatomical.Harmonize") | |
| 200301-22:23:54,846 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT2w.ComputeIQMs.harmonize". | |
| 2020-03-01 22:23:54,846 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT2w.ComputeIQMs.harmonize". | |
| 2020-03-01 22:25:08,279 niworkflows:INFO Successful spatial normalization (retry #1). | |
| 2020-03-01 22:25:11,551 niworkflows:INFO Report - setting fixed (/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT2w/SpatialNormalization/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/SpatialNormalization/fixed_masked.nii.gz) and moving (/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT2w/SpatialNormalization/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/SpatialNormalization/ants_t1_to_mni_Warped.nii.gz) images | |
| 2020-03-01 22:25:11,551 niworkflows:INFO Generating visual report | |
| 200301-22:25:18,998 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT2w.SpatialNormalization.SpatialNormalization". | |
| 2020-03-01 22:25:18,998 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT2w.SpatialNormalization.SpatialNormalization". | |
| 200301-22:25:20,563 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.AirMaskWorkflow.invert_xfm" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT2w/AirMaskWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/invert_xfm". | |
| 2020-03-01 22:25:20,563 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.AirMaskWorkflow.invert_xfm" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT2w/AirMaskWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/invert_xfm". | |
| 200301-22:25:20,566 nipype.workflow INFO: | |
| [Node] Running "invert_xfm" ("nipype.interfaces.ants.resampling.ApplyTransforms"), a CommandLine Interface with command: | |
| antsApplyTransforms --default-value 0 --dimensionality 3 --float 1 --input /opt/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-01_desc-head_mask.nii.gz --interpolation MultiLabel --output tpl-MNI152NLin2009cAsym_res-01_desc-head_mask_trans.nii.gz --reference-image /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT2w/AFNISkullStripWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/binarize/sub-01_ses-01_T2w_conformed_calc_thresh.nii.gz --transform /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT2w/SpatialNormalization/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/SpatialNormalization/ants_t1_to_mniInverseComposite.h5 | |
| 2020-03-01 22:25:20,566 nipype.workflow:INFO [Node] Running "invert_xfm" ("nipype.interfaces.ants.resampling.ApplyTransforms"), a CommandLine Interface with command: | |
| antsApplyTransforms --default-value 0 --dimensionality 3 --float 1 --input /opt/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-01_desc-head_mask.nii.gz --interpolation MultiLabel --output tpl-MNI152NLin2009cAsym_res-01_desc-head_mask_trans.nii.gz --reference-image /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT2w/AFNISkullStripWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/binarize/sub-01_ses-01_T2w_conformed_calc_thresh.nii.gz --transform /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT2w/SpatialNormalization/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/SpatialNormalization/ants_t1_to_mniInverseComposite.h5 | |
| 200301-22:25:22,558 nipype.workflow INFO: | |
| [Node] Setting-up "_MNItpms2t10" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT2w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/MNItpms2t1/mapflow/_MNItpms2t10". | |
| 2020-03-01 22:25:22,558 nipype.workflow:INFO [Node] Setting-up "_MNItpms2t10" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT2w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/MNItpms2t1/mapflow/_MNItpms2t10". | |
| 200301-22:25:22,561 nipype.workflow INFO: | |
| [Node] Running "_MNItpms2t10" ("nipype.interfaces.ants.resampling.ApplyTransforms"), a CommandLine Interface with command: | |
| antsApplyTransforms --default-value 0 --dimensionality 3 --float 1 --input /opt/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-01_label-CSF_probseg.nii.gz --interpolation Linear --output tpl-MNI152NLin2009cAsym_res-01_label-CSF_probseg_trans.nii.gz --reference-image /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT2w/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/conform/sub-01_ses-01_T2w_conformed.nii.gz --transform /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT2w/SpatialNormalization/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/SpatialNormalization/ants_t1_to_mniInverseComposite.h5 | |
| 2020-03-01 22:25:22,561 nipype.workflow:INFO [Node] Running "_MNItpms2t10" ("nipype.interfaces.ants.resampling.ApplyTransforms"), a CommandLine Interface with command: | |
| antsApplyTransforms --default-value 0 --dimensionality 3 --float 1 --input /opt/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-01_label-CSF_probseg.nii.gz --interpolation Linear --output tpl-MNI152NLin2009cAsym_res-01_label-CSF_probseg_trans.nii.gz --reference-image /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT2w/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/conform/sub-01_ses-01_T2w_conformed.nii.gz --transform /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT2w/SpatialNormalization/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/SpatialNormalization/ants_t1_to_mniInverseComposite.h5 | |
| 200301-22:25:22,571 nipype.workflow INFO: | |
| [Node] Setting-up "_MNItpms2t11" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT2w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/MNItpms2t1/mapflow/_MNItpms2t11". | |
| 2020-03-01 22:25:22,571 nipype.workflow:INFO [Node] Setting-up "_MNItpms2t11" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT2w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/MNItpms2t1/mapflow/_MNItpms2t11". | |
| 200301-22:25:22,575 nipype.workflow INFO: | |
| [Node] Running "_MNItpms2t11" ("nipype.interfaces.ants.resampling.ApplyTransforms"), a CommandLine Interface with command: | |
| antsApplyTransforms --default-value 0 --dimensionality 3 --float 1 --input /opt/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-01_label-GM_probseg.nii.gz --interpolation Linear --output tpl-MNI152NLin2009cAsym_res-01_label-GM_probseg_trans.nii.gz --reference-image /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT2w/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/conform/sub-01_ses-01_T2w_conformed.nii.gz --transform /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT2w/SpatialNormalization/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/SpatialNormalization/ants_t1_to_mniInverseComposite.h5 | |
| 2020-03-01 22:25:22,575 nipype.workflow:INFO [Node] Running "_MNItpms2t11" ("nipype.interfaces.ants.resampling.ApplyTransforms"), a CommandLine Interface with command: | |
| antsApplyTransforms --default-value 0 --dimensionality 3 --float 1 --input /opt/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-01_label-GM_probseg.nii.gz --interpolation Linear --output tpl-MNI152NLin2009cAsym_res-01_label-GM_probseg_trans.nii.gz --reference-image /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT2w/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/conform/sub-01_ses-01_T2w_conformed.nii.gz --transform /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT2w/SpatialNormalization/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/SpatialNormalization/ants_t1_to_mniInverseComposite.h5 | |
| 200301-22:25:28,968 nipype.workflow INFO: | |
| [Node] Finished "_MNItpms2t11". | |
| 2020-03-01 22:25:28,968 nipype.workflow:INFO [Node] Finished "_MNItpms2t11". | |
| 200301-22:25:30,625 nipype.workflow INFO: | |
| [Node] Setting-up "_MNItpms2t12" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT2w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/MNItpms2t1/mapflow/_MNItpms2t12". | |
| 2020-03-01 22:25:30,625 nipype.workflow:INFO [Node] Setting-up "_MNItpms2t12" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT2w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/MNItpms2t1/mapflow/_MNItpms2t12". | |
| 200301-22:25:30,628 nipype.workflow INFO: | |
| [Node] Running "_MNItpms2t12" ("nipype.interfaces.ants.resampling.ApplyTransforms"), a CommandLine Interface with command: | |
| antsApplyTransforms --default-value 0 --dimensionality 3 --float 1 --input /opt/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-01_label-WM_probseg.nii.gz --interpolation Linear --output tpl-MNI152NLin2009cAsym_res-01_label-WM_probseg_trans.nii.gz --reference-image /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT2w/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/conform/sub-01_ses-01_T2w_conformed.nii.gz --transform /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT2w/SpatialNormalization/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/SpatialNormalization/ants_t1_to_mniInverseComposite.h5 | |
| 2020-03-01 22:25:30,628 nipype.workflow:INFO [Node] Running "_MNItpms2t12" ("nipype.interfaces.ants.resampling.ApplyTransforms"), a CommandLine Interface with command: | |
| antsApplyTransforms --default-value 0 --dimensionality 3 --float 1 --input /opt/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-01_label-WM_probseg.nii.gz --interpolation Linear --output tpl-MNI152NLin2009cAsym_res-01_label-WM_probseg_trans.nii.gz --reference-image /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT2w/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/conform/sub-01_ses-01_T2w_conformed.nii.gz --transform /gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT2w/SpatialNormalization/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/SpatialNormalization/ants_t1_to_mniInverseComposite.h5 | |
| 200301-22:25:31,698 nipype.workflow INFO: | |
| [Node] Finished "_MNItpms2t10". | |
| 2020-03-01 22:25:31,698 nipype.workflow:INFO [Node] Finished "_MNItpms2t10". | |
| 200301-22:25:36,748 nipype.workflow INFO: | |
| [Node] Finished "_MNItpms2t12". | |
| 2020-03-01 22:25:36,748 nipype.workflow:INFO [Node] Finished "_MNItpms2t12". | |
| 200301-22:25:38,575 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.ComputeIQMs.MNItpms2t1" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT2w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/MNItpms2t1". | |
| 2020-03-01 22:25:38,575 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.ComputeIQMs.MNItpms2t1" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT2w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/MNItpms2t1". | |
| 200301-22:25:38,578 nipype.workflow INFO: | |
| [Node] Setting-up "_MNItpms2t10" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT2w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/MNItpms2t1/mapflow/_MNItpms2t10". | |
| 2020-03-01 22:25:38,578 nipype.workflow:INFO [Node] Setting-up "_MNItpms2t10" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT2w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/MNItpms2t1/mapflow/_MNItpms2t10". | |
| 200301-22:25:38,579 nipype.workflow INFO: | |
| [Node] Cached "_MNItpms2t10" - collecting precomputed outputs | |
| 2020-03-01 22:25:38,579 nipype.workflow:INFO [Node] Cached "_MNItpms2t10" - collecting precomputed outputs | |
| 200301-22:25:38,579 nipype.workflow INFO: | |
| [Node] "_MNItpms2t10" found cached. | |
| 2020-03-01 22:25:38,579 nipype.workflow:INFO [Node] "_MNItpms2t10" found cached. | |
| 200301-22:25:38,580 nipype.workflow INFO: | |
| [Node] Setting-up "_MNItpms2t11" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT2w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/MNItpms2t1/mapflow/_MNItpms2t11". | |
| 2020-03-01 22:25:38,580 nipype.workflow:INFO [Node] Setting-up "_MNItpms2t11" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT2w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/MNItpms2t1/mapflow/_MNItpms2t11". | |
| 200301-22:25:38,581 nipype.workflow INFO: | |
| [Node] Cached "_MNItpms2t11" - collecting precomputed outputs | |
| 2020-03-01 22:25:38,581 nipype.workflow:INFO [Node] Cached "_MNItpms2t11" - collecting precomputed outputs | |
| 200301-22:25:38,581 nipype.workflow INFO: | |
| [Node] "_MNItpms2t11" found cached. | |
| 2020-03-01 22:25:38,581 nipype.workflow:INFO [Node] "_MNItpms2t11" found cached. | |
| 200301-22:25:38,582 nipype.workflow INFO: | |
| [Node] Setting-up "_MNItpms2t12" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT2w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/MNItpms2t1/mapflow/_MNItpms2t12". | |
| 2020-03-01 22:25:38,582 nipype.workflow:INFO [Node] Setting-up "_MNItpms2t12" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT2w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/MNItpms2t1/mapflow/_MNItpms2t12". | |
| 200301-22:25:38,583 nipype.workflow INFO: | |
| [Node] Cached "_MNItpms2t12" - collecting precomputed outputs | |
| 2020-03-01 22:25:38,583 nipype.workflow:INFO [Node] Cached "_MNItpms2t12" - collecting precomputed outputs | |
| 200301-22:25:38,583 nipype.workflow INFO: | |
| [Node] "_MNItpms2t12" found cached. | |
| 2020-03-01 22:25:38,583 nipype.workflow:INFO [Node] "_MNItpms2t12" found cached. | |
| 200301-22:25:38,585 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT2w.ComputeIQMs.MNItpms2t1". | |
| 2020-03-01 22:25:38,585 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT2w.ComputeIQMs.MNItpms2t1". | |
| 200301-22:29:37,938 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT2w.AirMaskWorkflow.invert_xfm". | |
| 2020-03-01 22:29:37,938 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT2w.AirMaskWorkflow.invert_xfm". | |
| 200301-22:29:38,819 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.AirMaskWorkflow.ArtifactMask" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT2w/AirMaskWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/ArtifactMask". | |
| 2020-03-01 22:29:38,819 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.AirMaskWorkflow.ArtifactMask" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT2w/AirMaskWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/ArtifactMask". | |
| 200301-22:29:38,821 nipype.workflow INFO: | |
| [Node] Running "ArtifactMask" ("mriqc.interfaces.anatomical.ArtifactMask") | |
| 2020-03-01 22:29:38,821 nipype.workflow:INFO [Node] Running "ArtifactMask" ("mriqc.interfaces.anatomical.ArtifactMask") | |
| 200301-22:29:45,50 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT2w.AirMaskWorkflow.ArtifactMask". | |
| 2020-03-01 22:29:45,050 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT2w.AirMaskWorkflow.ArtifactMask". | |
| 200301-22:29:46,830 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.ComputeIQMs.ComputeQI2" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT2w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/ComputeQI2". | |
| 2020-03-01 22:29:46,830 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.ComputeIQMs.ComputeQI2" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT2w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/ComputeQI2". | |
| 200301-22:29:46,832 nipype.workflow INFO: | |
| [Node] Running "ComputeQI2" ("mriqc.interfaces.anatomical.ComputeQI2") | |
| 2020-03-01 22:29:46,832 nipype.workflow:INFO [Node] Running "ComputeQI2" ("mriqc.interfaces.anatomical.ComputeQI2") | |
| 200301-22:29:46,847 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.ComputeIQMs.measures" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT2w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/measures". | |
| 2020-03-01 22:29:46,847 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.ComputeIQMs.measures" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT2w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/measures". | |
| 200301-22:29:46,850 nipype.workflow INFO: | |
| [Node] Running "measures" ("mriqc.interfaces.anatomical.StructuralQC") | |
| 2020-03-01 22:29:46,850 nipype.workflow:INFO [Node] Running "measures" ("mriqc.interfaces.anatomical.StructuralQC") | |
| 200301-22:29:46,849 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.ComputeIQMs.provenance" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT2w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/provenance". | |
| 2020-03-01 22:29:46,849 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.ComputeIQMs.provenance" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT2w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/provenance". | |
| 200301-22:29:46,855 nipype.workflow INFO: | |
| [Node] Running "provenance" ("nipype.interfaces.utility.wrappers.Function") | |
| 2020-03-01 22:29:46,855 nipype.workflow:INFO [Node] Running "provenance" ("nipype.interfaces.utility.wrappers.Function") | |
| 200301-22:29:47,164 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT2w.ComputeIQMs.provenance". | |
| 2020-03-01 22:29:47,164 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT2w.ComputeIQMs.provenance". | |
| 200301-22:29:58,965 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT2w.ComputeIQMs.measures". | |
| 2020-03-01 22:29:58,965 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT2w.ComputeIQMs.measures". | |
| 200301-22:30:31,372 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT2w.ComputeIQMs.ComputeQI2". | |
| 2020-03-01 22:30:31,372 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT2w.ComputeIQMs.ComputeQI2". | |
| 200301-22:30:34,873 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.ReportsWorkflow.GenerateReport" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT2w/ReportsWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/GenerateReport". | |
| 2020-03-01 22:30:34,873 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.ReportsWorkflow.GenerateReport" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT2w/ReportsWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/GenerateReport". | |
| 200301-22:30:34,874 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.UploadMetrics" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT2w/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/UploadMetrics". | |
| 2020-03-01 22:30:34,874 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.UploadMetrics" in "/gpfs/scratchfs1/shj16108/hw3try2/hw3/work/workflow_enumerator/anatMRIQCT2w/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/UploadMetrics". | |
| 200301-22:30:34,876 nipype.workflow INFO: | |
| [Node] Running "GenerateReport" ("nipype.interfaces.utility.wrappers.Function") | |
| 2020-03-01 22:30:34,876 nipype.workflow:INFO [Node] Running "GenerateReport" ("nipype.interfaces.utility.wrappers.Function") | |
| 200301-22:30:34,878 nipype.workflow INFO: | |
| [Node] Running "UploadMetrics" ("mriqc.interfaces.webapi.UploadIQMs") | |
| 2020-03-01 22:30:34,878 nipype.workflow:INFO [Node] Running "UploadMetrics" ("mriqc.interfaces.webapi.UploadIQMs") | |
| 200301-22:30:34,879 nipype.interface INFO: | |
| MRIQC Web API: submitting to <https://mriqc.nimh.nih.gov:443/api/v1/T2w> | |
| 2020-03-01 22:30:34,879 nipype.interface:INFO MRIQC Web API: submitting to <https://mriqc.nimh.nih.gov:443/api/v1/T2w> | |
| 200301-22:30:35,9 nipype.interface INFO: | |
| QC metrics successfully uploaded. | |
| 2020-03-01 22:30:35,009 nipype.interface:INFO QC metrics successfully uploaded. | |
| 200301-22:30:35,11 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT2w.UploadMetrics". | |
| 2020-03-01 22:30:35,011 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT2w.UploadMetrics". | |
| 200301-22:30:35,75 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT2w.ReportsWorkflow.GenerateReport". | |
| 2020-03-01 22:30:35,075 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT2w.ReportsWorkflow.GenerateReport". | |
| 2020-03-01 22:30:38,867 mriqc:WARNING Anonymized quality metrics (IQMs) will be submitted to MRIQC's metrics repository. Submission of IQMs can be disabled using the ``--no-sub`` argument. Please visit https://mriqc.readthedocs.io/en/latest/dsa.html to revise MRIQC's Data Sharing Agreement. | |
| 2020-03-01 22:30:38,998 py.warnings:WARNING /usr/local/miniconda/lib/python3.7/site-packages/mriqc/reports/group.py:169: ResourceWarning: unclosed file <_io.TextIOWrapper name='/usr/local/miniconda/lib/python3.7/site-packages/mriqc/data/reports/embed_resources/boxplots.js' mode='r' encoding='UTF-8'> | |
| 'boxplots.js'))).read(), | |
| 2020-03-01 22:30:38,999 py.warnings:WARNING /usr/local/miniconda/lib/python3.7/site-packages/mriqc/reports/group.py:172: ResourceWarning: unclosed file <_io.TextIOWrapper name='/usr/local/miniconda/lib/python3.7/site-packages/mriqc/data/reports/embed_resources/d3.min.js' mode='r' encoding='UTF-8'> | |
| 'd3.min.js'))).read(), | |
| 2020-03-01 22:30:39,000 py.warnings:WARNING /usr/local/miniconda/lib/python3.7/site-packages/mriqc/reports/group.py:175: ResourceWarning: unclosed file <_io.TextIOWrapper name='/usr/local/miniconda/lib/python3.7/site-packages/mriqc/data/reports/embed_resources/boxplots.css' mode='r' encoding='UTF-8'> | |
| 'boxplots.css'))).read() | |