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| 2020-02-28 14:59:30,407 mriqc:IMPORTANT | |
| Running MRIQC version 0.15.0: | |
| * BIDS dataset path: /data. | |
| * Output folder: /out. | |
| * Analysis levels: group, participant. | |
| 2020-02-28 14:59:33,980 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) | |
| 2020-02-28 14:59:34,418 py.warnings:WARNING /usr/local/miniconda/lib/python3.7/site-packages/sklearn/metrics/classification.py:349: DeprecationWarning: invalid escape sequence \k | |
| """ | |
| 2020-02-28 14:59:34,422 py.warnings:WARNING /usr/local/miniconda/lib/python3.7/site-packages/sklearn/metrics/cluster/supervised.py:578: DeprecationWarning: invalid escape sequence \s | |
| """ | |
| 2020-02-28 14:59:35,360 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) | |
| 2020-02-28 14:59:36,148 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) | |
| 2020-02-28 14:59:37,165 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) | |
| 2020-02-28 14:59:37,260 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) | |
| 2020-02-28 14:59:37,272 py.warnings:WARNING /usr/local/miniconda/lib/python3.7/site-packages/sklearn/datasets/samples_generator.py:839: DeprecationWarning: invalid escape sequence \# | |
| """ | |
| 2020-02-28 14:59:37,272 py.warnings:WARNING /usr/local/miniconda/lib/python3.7/site-packages/sklearn/datasets/samples_generator.py:1429: DeprecationWarning: invalid escape sequence \c | |
| """ | |
| 2020-02-28 14:59:37,306 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 | |
| 2020-02-28 14:59:37,363 py.warnings:WARNING /usr/local/miniconda/lib/python3.7/site-packages/sklearn/decomposition/nmf.py:972: DeprecationWarning: invalid escape sequence \s | |
| """ | |
| 2020-02-28 14:59:37,439 py.warnings:WARNING /usr/local/miniconda/lib/python3.7/site-packages/sklearn/linear_model/omp.py:343: DeprecationWarning: invalid escape sequence \g | |
| """ | |
| 2020-02-28 14:59:37,606 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) | |
| 2020-02-28 14:59:37,763 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+) '\ | |
| 2020-02-28 14:59:38,080 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 | |
| 2020-02-28 14:59:38,121 py.warnings:WARNING /usr/local/miniconda/lib/python3.7/site-packages/networkx/generators/geometric.py:275: DeprecationWarning: invalid escape sequence \l | |
| """ | |
| 2020-02-28 14:59:38,156 py.warnings:WARNING /usr/local/miniconda/lib/python3.7/site-packages/networkx/algorithms/cluster.py:537: DeprecationWarning: invalid escape sequence \m | |
| """ | |
| 2020-02-28 14:59:38,237 py.warnings:WARNING /usr/local/miniconda/lib/python3.7/site-packages/networkx/algorithms/reciprocity.py:47: DeprecationWarning: invalid escape sequence \i | |
| """ | |
| 2020-02-28 14:59:38,245 py.warnings:WARNING /usr/local/miniconda/lib/python3.7/site-packages/networkx/algorithms/shortest_paths/weighted.py:1996: DeprecationWarning: invalid escape sequence \p | |
| """ | |
| 2020-02-28 14:59:38,367 py.warnings:WARNING /usr/local/miniconda/lib/python3.7/site-packages/networkx/generators/line.py:113: DeprecationWarning: invalid escape sequence \{ | |
| """ | |
| 2020-02-28 14:59:38,432 py.warnings:WARNING /usr/local/miniconda/lib/python3.7/site-packages/networkx/linalg/modularitymatrix.py:74: DeprecationWarning: invalid escape sequence \o | |
| """ | |
| 200228-14:59:38,726 nipype.workflow INFO: | |
| Building anatomical MRIQC workflow, datasets list: ['sub-01/ses-01/anat/sub-01_ses-01_T1w.nii.gz'] | |
| 2020-02-28 14:59:38,726 nipype.workflow:INFO Building anatomical MRIQC workflow, datasets list: ['sub-01/ses-01/anat/sub-01_ses-01_T1w.nii.gz'] | |
| 200228-14:59:38,866 nipype.workflow INFO: | |
| Building anatomical MRIQC workflow, datasets list: ['sub-01/ses-01/anat/sub-01_ses-01_T2w.nii.gz'] | |
| 2020-02-28 14:59:38,866 nipype.workflow:INFO Building anatomical MRIQC workflow, datasets list: ['sub-01/ses-01/anat/sub-01_ses-01_T2w.nii.gz'] | |
| 2020-02-28 14:59:48,144 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) | |
| 2020-02-28 14:59:48,182 py.warnings:WARNING /usr/local/miniconda/lib/python3.7/site-packages/sklearn/metrics/classification.py:349: DeprecationWarning: invalid escape sequence \k | |
| """ | |
| 2020-02-28 14:59:48,185 py.warnings:WARNING /usr/local/miniconda/lib/python3.7/site-packages/sklearn/metrics/cluster/supervised.py:578: DeprecationWarning: invalid escape sequence \s | |
| """ | |
| 2020-02-28 14:59:48,265 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]*' | |
| 2020-02-28 14:59:48,266 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]*' | |
| 2020-02-28 14:59:48,419 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) | |
| 2020-02-28 14:59:48,429 py.warnings:WARNING /usr/local/miniconda/lib/python3.7/site-packages/sklearn/datasets/samples_generator.py:839: DeprecationWarning: invalid escape sequence \# | |
| """ | |
| 2020-02-28 14:59:48,429 py.warnings:WARNING /usr/local/miniconda/lib/python3.7/site-packages/sklearn/datasets/samples_generator.py:1429: DeprecationWarning: invalid escape sequence \c | |
| """ | |
| 2020-02-28 14:59:48,454 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 | |
| 2020-02-28 14:59:48,494 py.warnings:WARNING /usr/local/miniconda/lib/python3.7/site-packages/sklearn/decomposition/nmf.py:972: DeprecationWarning: invalid escape sequence \s | |
| """ | |
| 2020-02-28 14:59:48,542 py.warnings:WARNING /usr/local/miniconda/lib/python3.7/site-packages/sklearn/linear_model/omp.py:343: DeprecationWarning: invalid escape sequence \g | |
| """ | |
| 2020-02-28 14:59:48,746 py.warnings:WARNING /usr/local/miniconda/lib/python3.7/site-packages/grabbit/core.py:780: DeprecationWarning: invalid escape sequence \{ | |
| to_rep = re.findall('\{(.*?)\}', template) | |
| 2020-02-28 14:59:48,746 py.warnings:WARNING /usr/local/miniconda/lib/python3.7/site-packages/grabbit/core.py:784: DeprecationWarning: invalid escape sequence \% | |
| template += '[^\%s]*$' % os.path.sep | |
| 2020-02-28 14:59:48,760 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+'], | |
| 2020-02-28 14:59:48,770 py.warnings:WARNING /usr/local/miniconda/lib/python3.7/site-packages/grabbit/extensions/writable.py:33: DeprecationWarning: invalid escape sequence \| | |
| match = re.search('([^|<]+)(<.*?>)?(\|.*)?', ent) | |
| 2020-02-28 14:59:48,770 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) | |
| 2020-02-28 14:59:48,901 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. | |
| 2020-02-28 14:59:49,470 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) | |
| 2020-02-28 14:59:52,008 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) | |
| 200228-14:59:57,729 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.funcMRIQC.non_steady_state_detector" in "/gpfs/scratchfs1/jac18015/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". | |
| 200228-14:59:57,744 nipype.workflow INFO: | |
| [Node] Running "non_steady_state_detector" ("nipype.algorithms.confounds.NonSteadyStateDetector") | |
| 200228-15:00:05,327 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.conform" in "/gpfs/scratchfs1/jac18015/hw3/work/workflow_enumerator/anatMRIQCT1w/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/conform". | |
| 2020-02-28 15:00:05,327 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.conform" in "/gpfs/scratchfs1/jac18015/hw3/work/workflow_enumerator/anatMRIQCT1w/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/conform". | |
| 200228-15:00:05,350 nipype.workflow INFO: | |
| [Node] Running "conform" ("mriqc.interfaces.common.ConformImage") | |
| 2020-02-28 15:00:05,350 nipype.workflow:INFO [Node] Running "conform" ("mriqc.interfaces.common.ConformImage") | |
| 200228-15:00:08,17 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.ComputeIQMs.metadata" in "/gpfs/scratchfs1/jac18015/hw3/work/workflow_enumerator/anatMRIQCT1w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/metadata". | |
| 200228-15:00:08,47 nipype.workflow INFO: | |
| [Node] Running "metadata" ("niworkflows.interfaces.bids.ReadSidecarJSON") | |
| 200228-15:00:08,154 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT1w.ComputeIQMs.metadata". | |
| 200228-15:00:08,665 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT1w.conform". | |
| 2020-02-28 15:00:08,665 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT1w.conform". | |
| 200228-15:00:09,175 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.funcMRIQC.non_steady_state_detector". | |
| 200228-15:00:10,102 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.funcMRIQC.sanitize" in "/gpfs/scratchfs1/jac18015/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". | |
| 200228-15:00:10,104 nipype.workflow INFO: | |
| [Node] Running "sanitize" ("niworkflows.interfaces.utils.SanitizeImage") | |
| 200228-15:00:10,115 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.ReportsWorkflow.PlotMosaicNoise" in "/gpfs/scratchfs1/jac18015/hw3/work/workflow_enumerator/anatMRIQCT1w/ReportsWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/PlotMosaicNoise". | |
| 2020-02-28 15:00:10,115 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.ReportsWorkflow.PlotMosaicNoise" in "/gpfs/scratchfs1/jac18015/hw3/work/workflow_enumerator/anatMRIQCT1w/ReportsWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/PlotMosaicNoise". | |
| 200228-15:00:10,118 nipype.workflow INFO: | |
| [Node] Running "PlotMosaicNoise" ("mriqc.interfaces.viz.PlotMosaic") | |
| 2020-02-28 15:00:10,118 nipype.workflow:INFO [Node] Running "PlotMosaicNoise" ("mriqc.interfaces.viz.PlotMosaic") | |
| 200228-15:00:15,629 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.AirMaskWorkflow.RotationMask" in "/gpfs/scratchfs1/jac18015/hw3/work/workflow_enumerator/anatMRIQCT1w/AirMaskWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/RotationMask". | |
| 2020-02-28 15:00:15,629 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.AirMaskWorkflow.RotationMask" in "/gpfs/scratchfs1/jac18015/hw3/work/workflow_enumerator/anatMRIQCT1w/AirMaskWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/RotationMask". | |
| 200228-15:00:15,660 nipype.workflow INFO: | |
| [Node] Running "RotationMask" ("mriqc.interfaces.anatomical.RotationMask") | |
| 2020-02-28 15:00:15,660 nipype.workflow:INFO [Node] Running "RotationMask" ("mriqc.interfaces.anatomical.RotationMask") | |
| 200228-15:00:21,398 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT1w.AirMaskWorkflow.RotationMask". | |
| 2020-02-28 15:00:21,398 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT1w.AirMaskWorkflow.RotationMask". | |
| 200228-15:00:22,240 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.AFNISkullStripWorkflow.inu_n4" in "/gpfs/scratchfs1/jac18015/hw3/work/workflow_enumerator/anatMRIQCT1w/AFNISkullStripWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/inu_n4". | |
| 2020-02-28 15:00:22,240 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.AFNISkullStripWorkflow.inu_n4" in "/gpfs/scratchfs1/jac18015/hw3/work/workflow_enumerator/anatMRIQCT1w/AFNISkullStripWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/inu_n4". | |
| 200228-15:00:22,249 nipype.workflow INFO: | |
| [Node] Running "inu_n4" ("nipype.interfaces.ants.segmentation.N4BiasFieldCorrection"), a CommandLine Interface with command: | |
| N4BiasFieldCorrection -d 3 --input-image /gpfs/scratchfs1/jac18015/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 ] | |
| 2020-02-28 15:00:22,249 nipype.workflow:INFO [Node] Running "inu_n4" ("nipype.interfaces.ants.segmentation.N4BiasFieldCorrection"), a CommandLine Interface with command: | |
| N4BiasFieldCorrection -d 3 --input-image /gpfs/scratchfs1/jac18015/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 ] | |
| 200228-15:00:52,397 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT1w.ReportsWorkflow.PlotMosaicNoise". | |
| 2020-02-28 15:00:52,397 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT1w.ReportsWorkflow.PlotMosaicNoise". | |
| 200228-15:00:54,281 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.conform" in "/gpfs/scratchfs1/jac18015/hw3/work/workflow_enumerator/anatMRIQCT2w/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/conform". | |
| 2020-02-28 15:00:54,281 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.conform" in "/gpfs/scratchfs1/jac18015/hw3/work/workflow_enumerator/anatMRIQCT2w/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/conform". | |
| 200228-15:00:54,284 nipype.workflow INFO: | |
| [Node] Running "conform" ("mriqc.interfaces.common.ConformImage") | |
| 2020-02-28 15:00:54,284 nipype.workflow:INFO [Node] Running "conform" ("mriqc.interfaces.common.ConformImage") | |
| 200228-15:00:57,498 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT2w.conform". | |
| 2020-02-28 15:00:57,498 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT2w.conform". | |
| 200228-15:00:58,277 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.ReportsWorkflow.PlotMosaicNoise" in "/gpfs/scratchfs1/jac18015/hw3/work/workflow_enumerator/anatMRIQCT2w/ReportsWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/PlotMosaicNoise". | |
| 2020-02-28 15:00:58,277 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.ReportsWorkflow.PlotMosaicNoise" in "/gpfs/scratchfs1/jac18015/hw3/work/workflow_enumerator/anatMRIQCT2w/ReportsWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/PlotMosaicNoise". | |
| 200228-15:00:58,294 nipype.workflow INFO: | |
| [Node] Running "PlotMosaicNoise" ("mriqc.interfaces.viz.PlotMosaic") | |
| 2020-02-28 15:00:58,294 nipype.workflow:INFO [Node] Running "PlotMosaicNoise" ("mriqc.interfaces.viz.PlotMosaic") | |
| 200228-15:01:07,906 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.funcMRIQC.sanitize". | |
| 200228-15:01:08,281 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.funcMRIQC.ReportsWorkflow.SpikesMask" in "/gpfs/scratchfs1/jac18015/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". | |
| 200228-15:01:08,320 nipype.workflow INFO: | |
| [Node] Running "SpikesMask" ("nipype.interfaces.utility.wrappers.Function") | |
| 200228-15:01:25,716 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.funcMRIQC.ReportsWorkflow.SpikesMask". | |
| 200228-15:01:26,371 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.funcMRIQC.ReportsWorkflow.SpikesFinderBgMask" in "/gpfs/scratchfs1/jac18015/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". | |
| 2020-02-28 15:01:26,371 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.funcMRIQC.ReportsWorkflow.SpikesFinderBgMask" in "/gpfs/scratchfs1/jac18015/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". | |
| 200228-15:01:26,388 nipype.workflow INFO: | |
| [Node] Running "SpikesFinderBgMask" ("mriqc.interfaces.functional.Spikes") | |
| 2020-02-28 15:01:26,388 nipype.workflow:INFO [Node] Running "SpikesFinderBgMask" ("mriqc.interfaces.functional.Spikes") | |
| 200228-15:01:39,274 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT2w.ReportsWorkflow.PlotMosaicNoise". | |
| 2020-02-28 15:01:39,274 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT2w.ReportsWorkflow.PlotMosaicNoise". | |
| 200228-15:01:43,760 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.funcMRIQC.fMRI_HMC_afni.gen_ref" in "/gpfs/scratchfs1/jac18015/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". | |
| 2020-02-28 15:01:43,760 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.funcMRIQC.fMRI_HMC_afni.gen_ref" in "/gpfs/scratchfs1/jac18015/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". | |
| 200228-15:01:43,786 nipype.workflow INFO: | |
| [Node] Running "gen_ref" ("niworkflows.interfaces.registration.EstimateReferenceImage") | |
| 2020-02-28 15:01:43,786 nipype.workflow:INFO [Node] Running "gen_ref" ("niworkflows.interfaces.registration.EstimateReferenceImage") | |
| 200228-15:01:48,0 nipype.interface INFO: | |
| stderr 2020-02-28T15:01:48.000141:++ 3dvolreg: AFNI version=AFNI_17.3.03 (Nov 9 2017) [64-bit] | |
| 2020-02-28 15:01:48,000 nipype.interface:INFO stderr 2020-02-28T15:01:48.000141:++ 3dvolreg: AFNI version=AFNI_17.3.03 (Nov 9 2017) [64-bit] | |
| 200228-15:01:48,0 nipype.interface INFO: | |
| stderr 2020-02-28T15:01:48.000542:++ Authored by: RW Cox | |
| 2020-02-28 15:01:48,000 nipype.interface:INFO stderr 2020-02-28T15:01:48.000542:++ Authored by: RW Cox | |
| 200228-15:01:48,15 nipype.interface INFO: | |
| stderr 2020-02-28T15:01:48.015333:[7m*+ WARNING:[0m If you are performing spatial transformations on an oblique dset, | |
| 2020-02-28 15:01:48,015 nipype.interface:INFO stderr 2020-02-28T15:01:48.015333:[7m*+ WARNING:[0m If you are performing spatial transformations on an oblique dset, | |
| 200228-15:01:48,15 nipype.interface INFO: | |
| stderr 2020-02-28T15:01:48.015333: such as /gpfs/scratchfs1/jac18015/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, | |
| 2020-02-28 15:01:48,015 nipype.interface:INFO stderr 2020-02-28T15:01:48.015333: such as /gpfs/scratchfs1/jac18015/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, | |
| 200228-15:01:48,15 nipype.interface INFO: | |
| stderr 2020-02-28T15:01:48.015333: or viewing/combining it with volumes of differing obliquity, | |
| 2020-02-28 15:01:48,015 nipype.interface:INFO stderr 2020-02-28T15:01:48.015333: or viewing/combining it with volumes of differing obliquity, | |
| 200228-15:01:48,15 nipype.interface INFO: | |
| stderr 2020-02-28T15:01:48.015333: you should consider running: | |
| 2020-02-28 15:01:48,015 nipype.interface:INFO stderr 2020-02-28T15:01:48.015333: you should consider running: | |
| 200228-15:01:48,15 nipype.interface INFO: | |
| stderr 2020-02-28T15:01:48.015333: 3dWarp -deoblique | |
| 2020-02-28 15:01:48,015 nipype.interface:INFO stderr 2020-02-28T15:01:48.015333: 3dWarp -deoblique | |
| 200228-15:01:48,15 nipype.interface INFO: | |
| stderr 2020-02-28T15:01:48.015333: on this and other oblique datasets in the same session. | |
| 2020-02-28 15:01:48,015 nipype.interface:INFO stderr 2020-02-28T15:01:48.015333: on this and other oblique datasets in the same session. | |
| 200228-15:01:48,15 nipype.interface INFO: | |
| stderr 2020-02-28T15:01:48.015333: See 3dWarp -help for details. | |
| 2020-02-28 15:01:48,015 nipype.interface:INFO stderr 2020-02-28T15:01:48.015333: See 3dWarp -help for details. | |
| 200228-15:01:48,22 nipype.interface INFO: | |
| stderr 2020-02-28T15:01:48.022967:++ Oblique dataset:/gpfs/scratchfs1/jac18015/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. | |
| 2020-02-28 15:01:48,022 nipype.interface:INFO stderr 2020-02-28T15:01:48.022967:++ Oblique dataset:/gpfs/scratchfs1/jac18015/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. | |
| 200228-15:01:48,23 nipype.interface INFO: | |
| stderr 2020-02-28T15:01:48.023108:++ Coarse del was 10, replaced with 6 | |
| 2020-02-28 15:01:48,023 nipype.interface:INFO stderr 2020-02-28T15:01:48.023108:++ Coarse del was 10, replaced with 6 | |
| 200228-15:01:53,864 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.funcMRIQC.ReportsWorkflow.SpikesFinderBgMask". | |
| 2020-02-28 15:01:53,864 nipype.workflow:INFO [Node] Finished "workflow_enumerator.funcMRIQC.ReportsWorkflow.SpikesFinderBgMask". | |
| 200228-15:01:54,341 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.AirMaskWorkflow.RotationMask" in "/gpfs/scratchfs1/jac18015/hw3/work/workflow_enumerator/anatMRIQCT2w/AirMaskWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/RotationMask". | |
| 2020-02-28 15:01:54,341 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.AirMaskWorkflow.RotationMask" in "/gpfs/scratchfs1/jac18015/hw3/work/workflow_enumerator/anatMRIQCT2w/AirMaskWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/RotationMask". | |
| 200228-15:01:54,350 nipype.workflow INFO: | |
| [Node] Running "RotationMask" ("mriqc.interfaces.anatomical.RotationMask") | |
| 2020-02-28 15:01:54,350 nipype.workflow:INFO [Node] Running "RotationMask" ("mriqc.interfaces.anatomical.RotationMask") | |
| 200228-15:02:00,228 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT2w.AirMaskWorkflow.RotationMask". | |
| 2020-02-28 15:02:00,228 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT2w.AirMaskWorkflow.RotationMask". | |
| 200228-15:02:02,341 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.AFNISkullStripWorkflow.inu_n4" in "/gpfs/scratchfs1/jac18015/hw3/work/workflow_enumerator/anatMRIQCT2w/AFNISkullStripWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/inu_n4". | |
| 2020-02-28 15:02:02,341 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.AFNISkullStripWorkflow.inu_n4" in "/gpfs/scratchfs1/jac18015/hw3/work/workflow_enumerator/anatMRIQCT2w/AFNISkullStripWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/inu_n4". | |
| 200228-15:02:02,344 nipype.workflow INFO: | |
| [Node] Running "inu_n4" ("nipype.interfaces.ants.segmentation.N4BiasFieldCorrection"), a CommandLine Interface with command: | |
| N4BiasFieldCorrection -d 3 --input-image /gpfs/scratchfs1/jac18015/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 ] | |
| 2020-02-28 15:02:02,344 nipype.workflow:INFO [Node] Running "inu_n4" ("nipype.interfaces.ants.segmentation.N4BiasFieldCorrection"), a CommandLine Interface with command: | |
| N4BiasFieldCorrection -d 3 --input-image /gpfs/scratchfs1/jac18015/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 ] | |
| 200228-15:03:40,708 nipype.interface INFO: | |
| stderr 2020-02-28T15:03:40.707994:++ Max displacement in automask = 1.03 (mm) at sub-brick 16 | |
| 2020-02-28 15:03:40,708 nipype.interface:INFO stderr 2020-02-28T15:03:40.707994:++ Max displacement in automask = 1.03 (mm) at sub-brick 16 | |
| 200228-15:03:40,708 nipype.interface INFO: | |
| stderr 2020-02-28T15:03:40.708230:++ Max delta displ in automask = 0.79 (mm) at sub-brick 17 | |
| 2020-02-28 15:03:40,708 nipype.interface:INFO stderr 2020-02-28T15:03:40.708230:++ Max delta displ in automask = 0.79 (mm) at sub-brick 17 | |
| 200228-15:03:46,314 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.funcMRIQC.fMRI_HMC_afni.gen_ref". | |
| 2020-02-28 15:03:46,314 nipype.workflow:INFO [Node] Finished "workflow_enumerator.funcMRIQC.fMRI_HMC_afni.gen_ref". | |
| 200228-15:03:48,447 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.funcMRIQC.fMRI_HMC_afni.motion_correct" in "/gpfs/scratchfs1/jac18015/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". | |
| 2020-02-28 15:03:48,447 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.funcMRIQC.fMRI_HMC_afni.motion_correct" in "/gpfs/scratchfs1/jac18015/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". | |
| 200228-15:03:48,471 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/jac18015/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/jac18015/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 | |
| 2020-02-28 15:03:48,471 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/jac18015/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/jac18015/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 | |
| 200228-15:19:59,373 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT1w.AFNISkullStripWorkflow.inu_n4". | |
| 2020-02-28 15:19:59,373 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT1w.AFNISkullStripWorkflow.inu_n4". | |
| 200228-15:20:01,707 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.HeadMaskWorkflow.fsl_bet" in "/gpfs/scratchfs1/jac18015/hw3/work/workflow_enumerator/anatMRIQCT1w/HeadMaskWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/fsl_bet". | |
| 2020-02-28 15:20:01,707 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.HeadMaskWorkflow.fsl_bet" in "/gpfs/scratchfs1/jac18015/hw3/work/workflow_enumerator/anatMRIQCT1w/HeadMaskWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/fsl_bet". | |
| 200228-15:20:01,734 nipype.workflow INFO: | |
| [Node] Running "fsl_bet" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command: | |
| bet /gpfs/scratchfs1/jac18015/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/jac18015/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 | |
| 2020-02-28 15:20:01,734 nipype.workflow:INFO [Node] Running "fsl_bet" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command: | |
| bet /gpfs/scratchfs1/jac18015/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/jac18015/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 | |
| 200228-15:21:45,933 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT2w.AFNISkullStripWorkflow.inu_n4". | |
| 2020-02-28 15:21:45,933 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT2w.AFNISkullStripWorkflow.inu_n4". | |
| 200228-15:21:47,513 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.AFNISkullStripWorkflow.skullstrip" in "/gpfs/scratchfs1/jac18015/hw3/work/workflow_enumerator/anatMRIQCT1w/AFNISkullStripWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/skullstrip". | |
| 2020-02-28 15:21:47,513 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.AFNISkullStripWorkflow.skullstrip" in "/gpfs/scratchfs1/jac18015/hw3/work/workflow_enumerator/anatMRIQCT1w/AFNISkullStripWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/skullstrip". | |
| 200228-15:21:47,516 nipype.workflow INFO: | |
| [Node] Running "skullstrip" ("nipype.interfaces.afni.preprocess.SkullStrip"), a CommandLine Interface with command: | |
| 3dSkullStrip -input /gpfs/scratchfs1/jac18015/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 | |
| 2020-02-28 15:21:47,516 nipype.workflow:INFO [Node] Running "skullstrip" ("nipype.interfaces.afni.preprocess.SkullStrip"), a CommandLine Interface with command: | |
| 3dSkullStrip -input /gpfs/scratchfs1/jac18015/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 | |
| 200228-15:25:39,384 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT1w.HeadMaskWorkflow.fsl_bet". | |
| 2020-02-28 15:25:39,384 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT1w.HeadMaskWorkflow.fsl_bet". | |
| 200228-15:25:39,744 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.HeadMaskWorkflow.fsl_bet" in "/gpfs/scratchfs1/jac18015/hw3/work/workflow_enumerator/anatMRIQCT2w/HeadMaskWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/fsl_bet". | |
| 2020-02-28 15:25:39,744 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.HeadMaskWorkflow.fsl_bet" in "/gpfs/scratchfs1/jac18015/hw3/work/workflow_enumerator/anatMRIQCT2w/HeadMaskWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/fsl_bet". | |
| 200228-15:25:39,747 nipype.workflow INFO: | |
| [Node] Running "fsl_bet" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command: | |
| bet /gpfs/scratchfs1/jac18015/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/jac18015/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 | |
| 2020-02-28 15:25:39,747 nipype.workflow:INFO [Node] Running "fsl_bet" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command: | |
| bet /gpfs/scratchfs1/jac18015/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/jac18015/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 | |
| 200228-15:25:44,939 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT1w.AFNISkullStripWorkflow.skullstrip". | |
| 2020-02-28 15:25:44,939 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT1w.AFNISkullStripWorkflow.skullstrip". | |
| 200228-15:25:45,758 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.AFNISkullStripWorkflow.sstrip_orig_vol" in "/gpfs/scratchfs1/jac18015/hw3/work/workflow_enumerator/anatMRIQCT1w/AFNISkullStripWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/sstrip_orig_vol". | |
| 2020-02-28 15:25:45,758 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.AFNISkullStripWorkflow.sstrip_orig_vol" in "/gpfs/scratchfs1/jac18015/hw3/work/workflow_enumerator/anatMRIQCT1w/AFNISkullStripWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/sstrip_orig_vol". | |
| 200228-15:25:45,761 nipype.workflow INFO: | |
| [Node] Running "sstrip_orig_vol" ("nipype.interfaces.afni.utils.Calc"), a CommandLine Interface with command: | |
| 3dcalc -a /gpfs/scratchfs1/jac18015/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/jac18015/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 | |
| 2020-02-28 15:25:45,761 nipype.workflow:INFO [Node] Running "sstrip_orig_vol" ("nipype.interfaces.afni.utils.Calc"), a CommandLine Interface with command: | |
| 3dcalc -a /gpfs/scratchfs1/jac18015/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/jac18015/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 | |
| 200228-15:25:51,422 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT1w.AFNISkullStripWorkflow.sstrip_orig_vol". | |
| 2020-02-28 15:25:51,422 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT1w.AFNISkullStripWorkflow.sstrip_orig_vol". | |
| 200228-15:25:51,755 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.segmentation" in "/gpfs/scratchfs1/jac18015/hw3/work/workflow_enumerator/anatMRIQCT1w/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/segmentation". | |
| 2020-02-28 15:25:51,755 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.segmentation" in "/gpfs/scratchfs1/jac18015/hw3/work/workflow_enumerator/anatMRIQCT1w/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/segmentation". | |
| 200228-15:25:51,759 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/jac18015/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 | |
| 2020-02-28 15:25:51,759 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/jac18015/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 | |
| 200228-15:31:25,645 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT2w.HeadMaskWorkflow.fsl_bet". | |
| 2020-02-28 15:31:25,645 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT2w.HeadMaskWorkflow.fsl_bet". | |
| 200228-15:31:26,87 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.AFNISkullStripWorkflow.binarize" in "/gpfs/scratchfs1/jac18015/hw3/work/workflow_enumerator/anatMRIQCT1w/AFNISkullStripWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/binarize". | |
| 2020-02-28 15:31:26,087 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.AFNISkullStripWorkflow.binarize" in "/gpfs/scratchfs1/jac18015/hw3/work/workflow_enumerator/anatMRIQCT1w/AFNISkullStripWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/binarize". | |
| 200228-15:31:26,91 nipype.workflow INFO: | |
| [Node] Running "binarize" ("nipype.interfaces.fsl.maths.Threshold"), a CommandLine Interface with command: | |
| fslmaths /gpfs/scratchfs1/jac18015/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/jac18015/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 | |
| 2020-02-28 15:31:26,091 nipype.workflow:INFO [Node] Running "binarize" ("nipype.interfaces.fsl.maths.Threshold"), a CommandLine Interface with command: | |
| fslmaths /gpfs/scratchfs1/jac18015/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/jac18015/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 | |
| 200228-15:31:30,183 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT1w.AFNISkullStripWorkflow.binarize". | |
| 2020-02-28 15:31:30,183 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT1w.AFNISkullStripWorkflow.binarize". | |
| 200228-15:31:32,100 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.ReportsWorkflow.PlotMosaicZoomed" in "/gpfs/scratchfs1/jac18015/hw3/work/workflow_enumerator/anatMRIQCT1w/ReportsWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/PlotMosaicZoomed". | |
| 2020-02-28 15:31:32,100 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.ReportsWorkflow.PlotMosaicZoomed" in "/gpfs/scratchfs1/jac18015/hw3/work/workflow_enumerator/anatMRIQCT1w/ReportsWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/PlotMosaicZoomed". | |
| 200228-15:31:32,103 nipype.workflow INFO: | |
| [Node] Running "PlotMosaicZoomed" ("mriqc.interfaces.viz.PlotMosaic") | |
| 2020-02-28 15:31:32,103 nipype.workflow:INFO [Node] Running "PlotMosaicZoomed" ("mriqc.interfaces.viz.PlotMosaic") | |
| 200228-15:32:07,813 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT1w.ReportsWorkflow.PlotMosaicZoomed". | |
| 2020-02-28 15:32:07,813 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT1w.ReportsWorkflow.PlotMosaicZoomed". | |
| 200228-15:32:08,136 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.ReportsWorkflow.MergePlots" in "/gpfs/scratchfs1/jac18015/hw3/work/workflow_enumerator/anatMRIQCT1w/ReportsWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/MergePlots". | |
| 2020-02-28 15:32:08,136 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.ReportsWorkflow.MergePlots" in "/gpfs/scratchfs1/jac18015/hw3/work/workflow_enumerator/anatMRIQCT1w/ReportsWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/MergePlots". | |
| 200228-15:32:08,139 nipype.workflow INFO: | |
| [Node] Running "MergePlots" ("nipype.interfaces.utility.base.Merge") | |
| 2020-02-28 15:32:08,139 nipype.workflow:INFO [Node] Running "MergePlots" ("nipype.interfaces.utility.base.Merge") | |
| 200228-15:32:08,142 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT1w.ReportsWorkflow.MergePlots". | |
| 2020-02-28 15:32:08,142 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT1w.ReportsWorkflow.MergePlots". | |
| 200228-15:32:10,674 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.ComputeIQMs.smoothness" in "/gpfs/scratchfs1/jac18015/hw3/work/workflow_enumerator/anatMRIQCT1w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/smoothness". | |
| 2020-02-28 15:32:10,674 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.ComputeIQMs.smoothness" in "/gpfs/scratchfs1/jac18015/hw3/work/workflow_enumerator/anatMRIQCT1w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/smoothness". | |
| 200228-15:32:10,688 nipype.workflow INFO: | |
| [Node] Running "smoothness" ("nipype.interfaces.afni.utils.FWHMx"), a CommandLine Interface with command: | |
| 3dFWHMx -ShowMeClassicFWHM -combine -detrend -input /gpfs/scratchfs1/jac18015/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/jac18015/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 | |
| 2020-02-28 15:32:10,688 nipype.workflow:INFO [Node] Running "smoothness" ("nipype.interfaces.afni.utils.FWHMx"), a CommandLine Interface with command: | |
| 3dFWHMx -ShowMeClassicFWHM -combine -detrend -input /gpfs/scratchfs1/jac18015/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/jac18015/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 | |
| 200228-15:32:44,56 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT1w.ComputeIQMs.smoothness". | |
| 2020-02-28 15:32:44,056 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT1w.ComputeIQMs.smoothness". | |
| 200228-15:32:48,387 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.SpatialNormalization.SpatialNormalization" in "/gpfs/scratchfs1/jac18015/hw3/work/workflow_enumerator/anatMRIQCT1w/SpatialNormalization/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/SpatialNormalization". | |
| 2020-02-28 15:32:48,387 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.SpatialNormalization.SpatialNormalization" in "/gpfs/scratchfs1/jac18015/hw3/work/workflow_enumerator/anatMRIQCT1w/SpatialNormalization/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/SpatialNormalization". | |
| 200228-15:32:48,407 nipype.workflow INFO: | |
| [Node] Running "SpatialNormalization" ("niworkflows.interfaces.registration.RobustMNINormalizationRPT") | |
| 2020-02-28 15:32:48,407 nipype.workflow:INFO [Node] Running "SpatialNormalization" ("niworkflows.interfaces.registration.RobustMNINormalizationRPT") | |
| 2020-02-28 15:32:53,560 niworkflows:INFO Estimating initial transform using AffineInitializer | |
| 2020-02-28 15:39:54,707 niworkflows:INFO Loading settings from file /usr/local/miniconda/lib/python3.7/site-packages/niworkflows/data/t1w-mni_registration_fast_000.json. | |
| 2020-02-28 15:39:54,723 niworkflows:INFO Retry #1, commandline: | |
| antsRegistration --collapse-output-transforms 1 --dimensionality 3 --float 0 --initial-moving-transform [ /gpfs/scratchfs1/jac18015/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/jac18015/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/jac18015/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/jac18015/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/jac18015/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/jac18015/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/jac18015/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 | |
| 200228-15:49:45,848 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT1w.segmentation". | |
| 2020-02-28 15:49:45,848 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT1w.segmentation". | |
| 200228-15:49:47,298 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.ComputeIQMs.harmonize" in "/gpfs/scratchfs1/jac18015/hw3/work/workflow_enumerator/anatMRIQCT1w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/harmonize". | |
| 2020-02-28 15:49:47,298 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.ComputeIQMs.harmonize" in "/gpfs/scratchfs1/jac18015/hw3/work/workflow_enumerator/anatMRIQCT1w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/harmonize". | |
| 200228-15:49:47,348 nipype.workflow INFO: | |
| [Node] Running "harmonize" ("mriqc.interfaces.anatomical.Harmonize") | |
| 2020-02-28 15:49:47,348 nipype.workflow:INFO [Node] Running "harmonize" ("mriqc.interfaces.anatomical.Harmonize") | |
| 200228-15:50:01,492 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT1w.ComputeIQMs.harmonize". | |
| 2020-02-28 15:50:01,492 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT1w.ComputeIQMs.harmonize". | |
| 200228-15:50:03,261 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.AFNISkullStripWorkflow.skullstrip" in "/gpfs/scratchfs1/jac18015/hw3/work/workflow_enumerator/anatMRIQCT2w/AFNISkullStripWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/skullstrip". | |
| 2020-02-28 15:50:03,261 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.AFNISkullStripWorkflow.skullstrip" in "/gpfs/scratchfs1/jac18015/hw3/work/workflow_enumerator/anatMRIQCT2w/AFNISkullStripWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/skullstrip". | |
| 200228-15:50:03,295 nipype.workflow INFO: | |
| [Node] Running "skullstrip" ("nipype.interfaces.afni.preprocess.SkullStrip"), a CommandLine Interface with command: | |
| 3dSkullStrip -input /gpfs/scratchfs1/jac18015/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 | |
| 2020-02-28 15:50:03,295 nipype.workflow:INFO [Node] Running "skullstrip" ("nipype.interfaces.afni.preprocess.SkullStrip"), a CommandLine Interface with command: | |
| 3dSkullStrip -input /gpfs/scratchfs1/jac18015/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 | |
| 2020-02-28 15:51:02,886 niworkflows:INFO Successful spatial normalization (retry #1). | |
| 2020-02-28 15:51:13,489 niworkflows:INFO Report - setting fixed (/gpfs/scratchfs1/jac18015/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/jac18015/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 | |
| 2020-02-28 15:51:13,489 niworkflows:INFO Generating visual report | |
| 200228-15:51:37,537 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT1w.SpatialNormalization.SpatialNormalization". | |
| 2020-02-28 15:51:37,537 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT1w.SpatialNormalization.SpatialNormalization". | |
| 200228-15:51:39,340 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.AirMaskWorkflow.invert_xfm" in "/gpfs/scratchfs1/jac18015/hw3/work/workflow_enumerator/anatMRIQCT1w/AirMaskWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/invert_xfm". | |
| 2020-02-28 15:51:39,340 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.AirMaskWorkflow.invert_xfm" in "/gpfs/scratchfs1/jac18015/hw3/work/workflow_enumerator/anatMRIQCT1w/AirMaskWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/invert_xfm". | |
| 200228-15:51:39,355 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/jac18015/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/jac18015/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 | |
| 2020-02-28 15:51:39,355 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/jac18015/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/jac18015/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 | |
| 200228-15:54:27,31 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT2w.AFNISkullStripWorkflow.skullstrip". | |
| 2020-02-28 15:54:27,031 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT2w.AFNISkullStripWorkflow.skullstrip". | |
| 200228-15:54:27,474 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.AFNISkullStripWorkflow.sstrip_orig_vol" in "/gpfs/scratchfs1/jac18015/hw3/work/workflow_enumerator/anatMRIQCT2w/AFNISkullStripWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/sstrip_orig_vol". | |
| 2020-02-28 15:54:27,474 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.AFNISkullStripWorkflow.sstrip_orig_vol" in "/gpfs/scratchfs1/jac18015/hw3/work/workflow_enumerator/anatMRIQCT2w/AFNISkullStripWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/sstrip_orig_vol". | |
| 200228-15:54:27,481 nipype.workflow INFO: | |
| [Node] Running "sstrip_orig_vol" ("nipype.interfaces.afni.utils.Calc"), a CommandLine Interface with command: | |
| 3dcalc -a /gpfs/scratchfs1/jac18015/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/jac18015/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 | |
| 2020-02-28 15:54:27,481 nipype.workflow:INFO [Node] Running "sstrip_orig_vol" ("nipype.interfaces.afni.utils.Calc"), a CommandLine Interface with command: | |
| 3dcalc -a /gpfs/scratchfs1/jac18015/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/jac18015/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 | |
| 200228-15:54:33,350 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT2w.AFNISkullStripWorkflow.sstrip_orig_vol". | |
| 2020-02-28 15:54:33,350 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT2w.AFNISkullStripWorkflow.sstrip_orig_vol". | |
| 200228-15:54:35,468 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.segmentation" in "/gpfs/scratchfs1/jac18015/hw3/work/workflow_enumerator/anatMRIQCT2w/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/segmentation". | |
| 2020-02-28 15:54:35,468 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.segmentation" in "/gpfs/scratchfs1/jac18015/hw3/work/workflow_enumerator/anatMRIQCT2w/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/segmentation". | |
| 200228-15:54:35,517 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/jac18015/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 | |
| 2020-02-28 15:54:35,517 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/jac18015/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 | |
| 200228-15:56:55,644 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.funcMRIQC.fMRI_HMC_afni.motion_correct". | |
| 2020-02-28 15:56:55,644 nipype.workflow:INFO [Node] Finished "workflow_enumerator.funcMRIQC.fMRI_HMC_afni.motion_correct". | |
| 200228-15:56:57,622 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.funcMRIQC.ComputeIQMs.quality" in "/gpfs/scratchfs1/jac18015/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". | |
| 2020-02-28 15:56:57,622 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.funcMRIQC.ComputeIQMs.quality" in "/gpfs/scratchfs1/jac18015/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". | |
| 200228-15:56:57,625 nipype.workflow INFO: | |
| [Node] Running "quality" ("nipype.interfaces.afni.preprocess.QualityIndex"), a CommandLine Interface with command: | |
| 3dTqual -automask /gpfs/scratchfs1/jac18015/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 | |
| 2020-02-28 15:56:57,625 nipype.workflow:INFO [Node] Running "quality" ("nipype.interfaces.afni.preprocess.QualityIndex"), a CommandLine Interface with command: | |
| 3dTqual -automask /gpfs/scratchfs1/jac18015/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 | |
| 200228-15:57:37,496 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.funcMRIQC.ComputeIQMs.quality". | |
| 2020-02-28 15:57:37,496 nipype.workflow:INFO [Node] Finished "workflow_enumerator.funcMRIQC.ComputeIQMs.quality". | |
| 200228-15:57:39,642 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.funcMRIQC.compute_tsnr" in "/gpfs/scratchfs1/jac18015/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". | |
| 2020-02-28 15:57:39,642 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.funcMRIQC.compute_tsnr" in "/gpfs/scratchfs1/jac18015/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". | |
| 200228-15:57:39,647 nipype.workflow INFO: | |
| [Node] Running "compute_tsnr" ("nipype.algorithms.confounds.TSNR") | |
| 2020-02-28 15:57:39,647 nipype.workflow:INFO [Node] Running "compute_tsnr" ("nipype.algorithms.confounds.TSNR") | |
| 200228-15:57:57,896 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.funcMRIQC.compute_tsnr". | |
| 2020-02-28 15:57:57,896 nipype.workflow:INFO [Node] Finished "workflow_enumerator.funcMRIQC.compute_tsnr". | |
| 200228-15:57:59,682 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.funcMRIQC.ReportsWorkflow.PlotMosaicSD" in "/gpfs/scratchfs1/jac18015/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". | |
| 2020-02-28 15:57:59,682 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.funcMRIQC.ReportsWorkflow.PlotMosaicSD" in "/gpfs/scratchfs1/jac18015/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". | |
| 200228-15:57:59,685 nipype.workflow INFO: | |
| [Node] Running "PlotMosaicSD" ("mriqc.interfaces.viz.PlotMosaic") | |
| 2020-02-28 15:57:59,685 nipype.workflow:INFO [Node] Running "PlotMosaicSD" ("mriqc.interfaces.viz.PlotMosaic") | |
| 200228-15:58:27,236 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.funcMRIQC.ReportsWorkflow.PlotMosaicSD". | |
| 2020-02-28 15:58:27,236 nipype.workflow:INFO [Node] Finished "workflow_enumerator.funcMRIQC.ReportsWorkflow.PlotMosaicSD". | |
| 200228-15:58:27,703 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.funcMRIQC.mean" in "/gpfs/scratchfs1/jac18015/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". | |
| 2020-02-28 15:58:27,703 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.funcMRIQC.mean" in "/gpfs/scratchfs1/jac18015/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". | |
| 200228-15:58:27,735 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/jac18015/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 | |
| 2020-02-28 15:58:27,735 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/jac18015/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 | |
| 200228-15:58:44,944 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.funcMRIQC.mean". | |
| 2020-02-28 15:58:44,944 nipype.workflow:INFO [Node] Finished "workflow_enumerator.funcMRIQC.mean". | |
| 200228-15:58:45,705 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.funcMRIQC.ReportsWorkflow.PlotMosaicMean" in "/gpfs/scratchfs1/jac18015/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". | |
| 2020-02-28 15:58:45,705 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.funcMRIQC.ReportsWorkflow.PlotMosaicMean" in "/gpfs/scratchfs1/jac18015/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". | |
| 200228-15:58:45,865 nipype.workflow INFO: | |
| [Node] Running "PlotMosaicMean" ("mriqc.interfaces.viz.PlotMosaic") | |
| 2020-02-28 15:58:45,865 nipype.workflow:INFO [Node] Running "PlotMosaicMean" ("mriqc.interfaces.viz.PlotMosaic") | |
| 200228-15:59:12,243 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.funcMRIQC.ReportsWorkflow.PlotMosaicMean". | |
| 2020-02-28 15:59:12,243 nipype.workflow:INFO [Node] Finished "workflow_enumerator.funcMRIQC.ReportsWorkflow.PlotMosaicMean". | |
| 200228-15:59:13,740 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.funcMRIQC.SpatialNormalization.SharpenEPI" in "/gpfs/scratchfs1/jac18015/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". | |
| 2020-02-28 15:59:13,740 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.funcMRIQC.SpatialNormalization.SharpenEPI" in "/gpfs/scratchfs1/jac18015/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". | |
| 200228-15:59:13,744 nipype.workflow INFO: | |
| [Node] Running "SharpenEPI" ("nipype.interfaces.ants.segmentation.N4BiasFieldCorrection"), a CommandLine Interface with command: | |
| N4BiasFieldCorrection -d 3 --input-image /gpfs/scratchfs1/jac18015/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 | |
| 2020-02-28 15:59:13,744 nipype.workflow:INFO [Node] Running "SharpenEPI" ("nipype.interfaces.ants.segmentation.N4BiasFieldCorrection"), a CommandLine Interface with command: | |
| N4BiasFieldCorrection -d 3 --input-image /gpfs/scratchfs1/jac18015/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 | |
| 200228-15:59:44,923 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.funcMRIQC.SpatialNormalization.SharpenEPI". | |
| 2020-02-28 15:59:44,923 nipype.workflow:INFO [Node] Finished "workflow_enumerator.funcMRIQC.SpatialNormalization.SharpenEPI". | |
| 200228-15:59:45,771 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.funcMRIQC.fMRIBrainMask.bet_msk" in "/gpfs/scratchfs1/jac18015/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". | |
| 2020-02-28 15:59:45,771 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.funcMRIQC.fMRIBrainMask.bet_msk" in "/gpfs/scratchfs1/jac18015/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". | |
| 200228-15:59:45,774 nipype.workflow INFO: | |
| [Node] Running "bet_msk" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command: | |
| bet /gpfs/scratchfs1/jac18015/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/jac18015/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 | |
| 2020-02-28 15:59:45,774 nipype.workflow:INFO [Node] Running "bet_msk" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command: | |
| bet /gpfs/scratchfs1/jac18015/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/jac18015/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 | |
| 200228-15:59:54,84 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.funcMRIQC.fMRIBrainMask.bet_msk". | |
| 2020-02-28 15:59:54,084 nipype.workflow:INFO [Node] Finished "workflow_enumerator.funcMRIQC.fMRIBrainMask.bet_msk". | |
| 200228-15:59:55,780 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.funcMRIQC.fMRIBrainMask.erode" in "/gpfs/scratchfs1/jac18015/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". | |
| 2020-02-28 15:59:55,780 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.funcMRIQC.fMRIBrainMask.erode" in "/gpfs/scratchfs1/jac18015/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". | |
| 200228-15:59:55,784 nipype.workflow INFO: | |
| [Node] Running "erode" ("nipype.interfaces.fsl.maths.ErodeImage"), a CommandLine Interface with command: | |
| fslmaths /gpfs/scratchfs1/jac18015/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/jac18015/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 | |
| 2020-02-28 15:59:55,784 nipype.workflow:INFO [Node] Running "erode" ("nipype.interfaces.fsl.maths.ErodeImage"), a CommandLine Interface with command: | |
| fslmaths /gpfs/scratchfs1/jac18015/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/jac18015/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 | |
| 200228-15:59:58,881 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.funcMRIQC.fMRIBrainMask.erode". | |
| 2020-02-28 15:59:58,881 nipype.workflow:INFO [Node] Finished "workflow_enumerator.funcMRIQC.fMRIBrainMask.erode". | |
| 200228-15:59:59,777 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.funcMRIQC.ComputeIQMs.gcor" in "/gpfs/scratchfs1/jac18015/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". | |
| 2020-02-28 15:59:59,777 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.funcMRIQC.ComputeIQMs.gcor" in "/gpfs/scratchfs1/jac18015/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". | |
| 200228-15:59:59,780 nipype.workflow INFO: | |
| [Node] Running "gcor" ("mriqc.interfaces.transitional.GCOR"), a CommandLine Interface with command: | |
| @compute_gcor -mask /gpfs/scratchfs1/jac18015/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/jac18015/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 | |
| 2020-02-28 15:59:59,780 nipype.workflow:INFO [Node] Running "gcor" ("mriqc.interfaces.transitional.GCOR"), a CommandLine Interface with command: | |
| @compute_gcor -mask /gpfs/scratchfs1/jac18015/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/jac18015/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 | |
| 200228-16:00:43,526 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.funcMRIQC.ComputeIQMs.gcor". | |
| 2020-02-28 16:00:43,526 nipype.workflow:INFO [Node] Finished "workflow_enumerator.funcMRIQC.ComputeIQMs.gcor". | |
| 200228-16:00:43,818 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.funcMRIQC.ComputeIQMs.outliers" in "/gpfs/scratchfs1/jac18015/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". | |
| 2020-02-28 16:00:43,818 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.funcMRIQC.ComputeIQMs.outliers" in "/gpfs/scratchfs1/jac18015/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". | |
| 200228-16:00:43,840 nipype.workflow INFO: | |
| [Node] Running "outliers" ("nipype.interfaces.afni.preprocess.OutlierCount"), a CommandLine Interface with command: | |
| 3dToutcount -fraction -mask /gpfs/scratchfs1/jac18015/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/jac18015/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 | |
| 2020-02-28 16:00:43,840 nipype.workflow:INFO [Node] Running "outliers" ("nipype.interfaces.afni.preprocess.OutlierCount"), a CommandLine Interface with command: | |
| 3dToutcount -fraction -mask /gpfs/scratchfs1/jac18015/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/jac18015/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 | |
| 200228-16:01:04,466 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.funcMRIQC.ComputeIQMs.outliers". | |
| 2020-02-28 16:01:04,466 nipype.workflow:INFO [Node] Finished "workflow_enumerator.funcMRIQC.ComputeIQMs.outliers". | |
| 200228-16:01:05,847 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.funcMRIQC.ComputeIQMs.smoothness" in "/gpfs/scratchfs1/jac18015/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". | |
| 2020-02-28 16:01:05,847 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.funcMRIQC.ComputeIQMs.smoothness" in "/gpfs/scratchfs1/jac18015/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". | |
| 200228-16:01:05,948 nipype.workflow INFO: | |
| [Node] Running "smoothness" ("nipype.interfaces.afni.utils.FWHMx"), a CommandLine Interface with command: | |
| 3dFWHMx -ShowMeClassicFWHM -combine -detrend -input /gpfs/scratchfs1/jac18015/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/jac18015/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 | |
| 2020-02-28 16:01:05,948 nipype.workflow:INFO [Node] Running "smoothness" ("nipype.interfaces.afni.utils.FWHMx"), a CommandLine Interface with command: | |
| 3dFWHMx -ShowMeClassicFWHM -combine -detrend -input /gpfs/scratchfs1/jac18015/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/jac18015/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 | |
| 200228-16:01:09,151 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.funcMRIQC.ComputeIQMs.smoothness". | |
| 2020-02-28 16:01:09,151 nipype.workflow:INFO [Node] Finished "workflow_enumerator.funcMRIQC.ComputeIQMs.smoothness". | |
| 200228-16:01:09,850 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.funcMRIQC.ComputeIQMs.ComputeDVARS" in "/gpfs/scratchfs1/jac18015/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". | |
| 2020-02-28 16:01:09,850 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.funcMRIQC.ComputeIQMs.ComputeDVARS" in "/gpfs/scratchfs1/jac18015/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". | |
| 200228-16:01:09,856 nipype.workflow INFO: | |
| [Node] Running "ComputeDVARS" ("nipype.algorithms.confounds.ComputeDVARS") | |
| 2020-02-28 16:01:09,856 nipype.workflow:INFO [Node] Running "ComputeDVARS" ("nipype.algorithms.confounds.ComputeDVARS") | |
| 200228-16:03:19,792 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.funcMRIQC.ComputeIQMs.ComputeDVARS". | |
| 2020-02-28 16:03:19,792 nipype.workflow:INFO [Node] Finished "workflow_enumerator.funcMRIQC.ComputeIQMs.ComputeDVARS". | |
| 200228-16:03:21,982 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.funcMRIQC.SpatialNormalization.EPI2MNI" in "/gpfs/scratchfs1/jac18015/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". | |
| 2020-02-28 16:03:21,982 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.funcMRIQC.SpatialNormalization.EPI2MNI" in "/gpfs/scratchfs1/jac18015/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". | |
| 200228-16:03:21,985 nipype.workflow INFO: | |
| [Node] Running "EPI2MNI" ("niworkflows.interfaces.registration.RobustMNINormalizationRPT") | |
| 2020-02-28 16:03:21,985 nipype.workflow:INFO [Node] Running "EPI2MNI" ("niworkflows.interfaces.registration.RobustMNINormalizationRPT") | |
| 2020-02-28 16:03:21,986 niworkflows:INFO Estimating initial transform using AffineInitializer | |
| 200228-16:04:57,696 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT1w.AirMaskWorkflow.invert_xfm". | |
| 2020-02-28 16:04:57,696 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT1w.AirMaskWorkflow.invert_xfm". | |
| 200228-16:04:58,76 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.funcMRIQC.fMRI_HMC_afni.ComputeFD" in "/gpfs/scratchfs1/jac18015/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". | |
| 2020-02-28 16:04:58,076 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.funcMRIQC.fMRI_HMC_afni.ComputeFD" in "/gpfs/scratchfs1/jac18015/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". | |
| 200228-16:04:58,178 nipype.workflow INFO: | |
| [Node] Running "ComputeFD" ("nipype.algorithms.confounds.FramewiseDisplacement") | |
| 2020-02-28 16:04:58,178 nipype.workflow:INFO [Node] Running "ComputeFD" ("nipype.algorithms.confounds.FramewiseDisplacement") | |
| 200228-16:04:58,262 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.funcMRIQC.fMRI_HMC_afni.ComputeFD". | |
| 2020-02-28 16:04:58,262 nipype.workflow:INFO [Node] Finished "workflow_enumerator.funcMRIQC.fMRI_HMC_afni.ComputeFD". | |
| 200228-16:05:00,116 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.funcMRIQC.ComputeIQMs.measures" in "/gpfs/scratchfs1/jac18015/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". | |
| 2020-02-28 16:05:00,116 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.funcMRIQC.ComputeIQMs.measures" in "/gpfs/scratchfs1/jac18015/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". | |
| 200228-16:05:00,146 nipype.workflow INFO: | |
| [Node] Running "measures" ("mriqc.interfaces.functional.FunctionalQC") | |
| 2020-02-28 16:05:00,146 nipype.workflow:INFO [Node] Running "measures" ("mriqc.interfaces.functional.FunctionalQC") | |
| 200228-16:05:15,246 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.funcMRIQC.ComputeIQMs.measures". | |
| 2020-02-28 16:05:15,246 nipype.workflow:INFO [Node] Finished "workflow_enumerator.funcMRIQC.ComputeIQMs.measures". | |
| 200228-16:05:16,410 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.AirMaskWorkflow.ArtifactMask" in "/gpfs/scratchfs1/jac18015/hw3/work/workflow_enumerator/anatMRIQCT1w/AirMaskWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/ArtifactMask". | |
| 2020-02-28 16:05:16,410 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.AirMaskWorkflow.ArtifactMask" in "/gpfs/scratchfs1/jac18015/hw3/work/workflow_enumerator/anatMRIQCT1w/AirMaskWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/ArtifactMask". | |
| 200228-16:05:16,412 nipype.workflow INFO: | |
| [Node] Running "ArtifactMask" ("mriqc.interfaces.anatomical.ArtifactMask") | |
| 2020-02-28 16:05:16,412 nipype.workflow:INFO [Node] Running "ArtifactMask" ("mriqc.interfaces.anatomical.ArtifactMask") | |
| 200228-16:05:37,138 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT1w.AirMaskWorkflow.ArtifactMask". | |
| 2020-02-28 16:05:37,138 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT1w.AirMaskWorkflow.ArtifactMask". | |
| 200228-16:05:38,105 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.funcMRIQC.UploadMetrics" in "/gpfs/scratchfs1/jac18015/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". | |
| 2020-02-28 16:05:38,105 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.funcMRIQC.UploadMetrics" in "/gpfs/scratchfs1/jac18015/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". | |
| 200228-16:05:38,140 nipype.workflow INFO: | |
| [Node] Running "UploadMetrics" ("mriqc.interfaces.webapi.UploadIQMs") | |
| 2020-02-28 16:05:38,140 nipype.workflow:INFO [Node] Running "UploadMetrics" ("mriqc.interfaces.webapi.UploadIQMs") | |
| 200228-16:05:39,546 nipype.interface INFO: | |
| MRIQC Web API: submitting to <https://mriqc.nimh.nih.gov:443/api/v1/bold> | |
| 2020-02-28 16:05:39,546 nipype.interface:INFO MRIQC Web API: submitting to <https://mriqc.nimh.nih.gov:443/api/v1/bold> | |
| 200228-16:05:39,731 nipype.interface INFO: | |
| QC metrics successfully uploaded. | |
| 2020-02-28 16:05:39,731 nipype.interface:INFO QC metrics successfully uploaded. | |
| 200228-16:05:39,734 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.funcMRIQC.UploadMetrics". | |
| 2020-02-28 16:05:39,734 nipype.workflow:INFO [Node] Finished "workflow_enumerator.funcMRIQC.UploadMetrics". | |
| 200228-16:05:40,126 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.ComputeIQMs.ComputeQI2" in "/gpfs/scratchfs1/jac18015/hw3/work/workflow_enumerator/anatMRIQCT1w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/ComputeQI2". | |
| 2020-02-28 16:05:40,126 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.ComputeIQMs.ComputeQI2" in "/gpfs/scratchfs1/jac18015/hw3/work/workflow_enumerator/anatMRIQCT1w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/ComputeQI2". | |
| 200228-16:05:40,135 nipype.workflow INFO: | |
| [Node] Running "ComputeQI2" ("mriqc.interfaces.anatomical.ComputeQI2") | |
| 2020-02-28 16:05:40,135 nipype.workflow:INFO [Node] Running "ComputeQI2" ("mriqc.interfaces.anatomical.ComputeQI2") | |
| 2020-02-28 16:07:13,599 niworkflows:INFO Terminal outputs of initialization saved (/gpfs/scratchfs1/jac18015/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). | |
| 2020-02-28 16:07:13,599 niworkflows:INFO Loading settings from file /usr/local/miniconda/lib/python3.7/site-packages/niworkflows/data/bold-mni_registration_precise_000.json. | |
| 2020-02-28 16:07:13,602 niworkflows:INFO Retry #1, commandline: | |
| antsRegistration --collapse-output-transforms 1 --dimensionality 3 --float 0 --initial-moving-transform [ /gpfs/scratchfs1/jac18015/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/jac18015/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/jac18015/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/jac18015/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/jac18015/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/jac18015/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/jac18015/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 | |
| 200228-16:07:40,704 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT1w.ComputeIQMs.ComputeQI2". | |
| 2020-02-28 16:07:40,704 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT1w.ComputeIQMs.ComputeQI2". | |
| 200228-16:07:42,248 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.ComputeIQMs.provenance" in "/gpfs/scratchfs1/jac18015/hw3/work/workflow_enumerator/anatMRIQCT1w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/provenance". | |
| 2020-02-28 16:07:42,248 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.ComputeIQMs.provenance" in "/gpfs/scratchfs1/jac18015/hw3/work/workflow_enumerator/anatMRIQCT1w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/provenance". | |
| 200228-16:07:42,250 nipype.workflow INFO: | |
| [Node] Running "provenance" ("nipype.interfaces.utility.wrappers.Function") | |
| 2020-02-28 16:07:42,250 nipype.workflow:INFO [Node] Running "provenance" ("nipype.interfaces.utility.wrappers.Function") | |
| 200228-16:07:42,797 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT1w.ComputeIQMs.provenance". | |
| 2020-02-28 16:07:42,797 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT1w.ComputeIQMs.provenance". | |
| 200228-16:07:44,309 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.AFNISkullStripWorkflow.binarize" in "/gpfs/scratchfs1/jac18015/hw3/work/workflow_enumerator/anatMRIQCT2w/AFNISkullStripWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/binarize". | |
| 2020-02-28 16:07:44,309 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.AFNISkullStripWorkflow.binarize" in "/gpfs/scratchfs1/jac18015/hw3/work/workflow_enumerator/anatMRIQCT2w/AFNISkullStripWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/binarize". | |
| 200228-16:07:44,311 nipype.workflow INFO: | |
| [Node] Running "binarize" ("nipype.interfaces.fsl.maths.Threshold"), a CommandLine Interface with command: | |
| fslmaths /gpfs/scratchfs1/jac18015/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/jac18015/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 | |
| 2020-02-28 16:07:44,311 nipype.workflow:INFO [Node] Running "binarize" ("nipype.interfaces.fsl.maths.Threshold"), a CommandLine Interface with command: | |
| fslmaths /gpfs/scratchfs1/jac18015/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/jac18015/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 | |
| 200228-16:07:48,885 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT2w.AFNISkullStripWorkflow.binarize". | |
| 2020-02-28 16:07:48,885 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT2w.AFNISkullStripWorkflow.binarize". | |
| 200228-16:07:50,257 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.ReportsWorkflow.PlotMosaicZoomed" in "/gpfs/scratchfs1/jac18015/hw3/work/workflow_enumerator/anatMRIQCT2w/ReportsWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/PlotMosaicZoomed". | |
| 2020-02-28 16:07:50,257 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.ReportsWorkflow.PlotMosaicZoomed" in "/gpfs/scratchfs1/jac18015/hw3/work/workflow_enumerator/anatMRIQCT2w/ReportsWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/PlotMosaicZoomed". | |
| 200228-16:07:50,277 nipype.workflow INFO: | |
| [Node] Running "PlotMosaicZoomed" ("mriqc.interfaces.viz.PlotMosaic") | |
| 2020-02-28 16:07:50,277 nipype.workflow:INFO [Node] Running "PlotMosaicZoomed" ("mriqc.interfaces.viz.PlotMosaic") | |
| 200228-16:08:26,848 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT2w.ReportsWorkflow.PlotMosaicZoomed". | |
| 2020-02-28 16:08:26,848 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT2w.ReportsWorkflow.PlotMosaicZoomed". | |
| 200228-16:08:28,306 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.ReportsWorkflow.MergePlots" in "/gpfs/scratchfs1/jac18015/hw3/work/workflow_enumerator/anatMRIQCT2w/ReportsWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/MergePlots". | |
| 2020-02-28 16:08:28,306 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.ReportsWorkflow.MergePlots" in "/gpfs/scratchfs1/jac18015/hw3/work/workflow_enumerator/anatMRIQCT2w/ReportsWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/MergePlots". | |
| 200228-16:08:28,314 nipype.workflow INFO: | |
| [Node] Running "MergePlots" ("nipype.interfaces.utility.base.Merge") | |
| 2020-02-28 16:08:28,314 nipype.workflow:INFO [Node] Running "MergePlots" ("nipype.interfaces.utility.base.Merge") | |
| 200228-16:08:28,317 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT2w.ReportsWorkflow.MergePlots". | |
| 2020-02-28 16:08:28,317 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT2w.ReportsWorkflow.MergePlots". | |
| 200228-16:08:30,271 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.ComputeIQMs.smoothness" in "/gpfs/scratchfs1/jac18015/hw3/work/workflow_enumerator/anatMRIQCT2w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/smoothness". | |
| 2020-02-28 16:08:30,271 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.ComputeIQMs.smoothness" in "/gpfs/scratchfs1/jac18015/hw3/work/workflow_enumerator/anatMRIQCT2w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/smoothness". | |
| 200228-16:08:30,275 nipype.workflow INFO: | |
| [Node] Running "smoothness" ("nipype.interfaces.afni.utils.FWHMx"), a CommandLine Interface with command: | |
| 3dFWHMx -ShowMeClassicFWHM -combine -detrend -input /gpfs/scratchfs1/jac18015/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/jac18015/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 | |
| 2020-02-28 16:08:30,275 nipype.workflow:INFO [Node] Running "smoothness" ("nipype.interfaces.afni.utils.FWHMx"), a CommandLine Interface with command: | |
| 3dFWHMx -ShowMeClassicFWHM -combine -detrend -input /gpfs/scratchfs1/jac18015/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/jac18015/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 | |
| 200228-16:09:02,210 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT2w.ComputeIQMs.smoothness". | |
| 2020-02-28 16:09:02,210 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT2w.ComputeIQMs.smoothness". | |
| 200228-16:09:04,321 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.SpatialNormalization.SpatialNormalization" in "/gpfs/scratchfs1/jac18015/hw3/work/workflow_enumerator/anatMRIQCT2w/SpatialNormalization/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/SpatialNormalization". | |
| 2020-02-28 16:09:04,321 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.SpatialNormalization.SpatialNormalization" in "/gpfs/scratchfs1/jac18015/hw3/work/workflow_enumerator/anatMRIQCT2w/SpatialNormalization/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/SpatialNormalization". | |
| 200228-16:09:04,323 nipype.workflow INFO: | |
| [Node] Running "SpatialNormalization" ("niworkflows.interfaces.registration.RobustMNINormalizationRPT") | |
| 2020-02-28 16:09:04,323 nipype.workflow:INFO [Node] Running "SpatialNormalization" ("niworkflows.interfaces.registration.RobustMNINormalizationRPT") | |
| 2020-02-28 16:09:09,719 niworkflows:INFO Estimating initial transform using AffineInitializer | |
| 2020-02-28 16:12:48,164 niworkflows:INFO Successful spatial normalization (retry #1). | |
| 2020-02-28 16:12:48,179 niworkflows:INFO Report - setting fixed (/opt/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz) and moving (/gpfs/scratchfs1/jac18015/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 | |
| 2020-02-28 16:12:48,179 niworkflows:INFO Generating visual report | |
| 200228-16:13:21,505 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.funcMRIQC.SpatialNormalization.EPI2MNI". | |
| 2020-02-28 16:13:21,505 nipype.workflow:INFO [Node] Finished "workflow_enumerator.funcMRIQC.SpatialNormalization.EPI2MNI". | |
| 200228-16:13:22,690 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.funcMRIQC.SpatialNormalization.ResampleSegmentation" in "/gpfs/scratchfs1/jac18015/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". | |
| 2020-02-28 16:13:22,690 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.funcMRIQC.SpatialNormalization.ResampleSegmentation" in "/gpfs/scratchfs1/jac18015/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". | |
| 200228-16:13:22,693 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/jac18015/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/jac18015/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 | |
| 2020-02-28 16:13:22,693 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/jac18015/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/jac18015/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 | |
| 200228-16:13:40,129 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.funcMRIQC.SpatialNormalization.ResampleSegmentation". | |
| 2020-02-28 16:13:40,129 nipype.workflow:INFO [Node] Finished "workflow_enumerator.funcMRIQC.SpatialNormalization.ResampleSegmentation". | |
| 200228-16:13:40,827 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.funcMRIQC.ReportsWorkflow.BigPlot" in "/gpfs/scratchfs1/jac18015/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". | |
| 2020-02-28 16:13:40,827 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.funcMRIQC.ReportsWorkflow.BigPlot" in "/gpfs/scratchfs1/jac18015/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". | |
| 200228-16:13:40,846 nipype.workflow INFO: | |
| [Node] Running "BigPlot" ("niworkflows.interfaces.plotting.FMRISummary") | |
| 2020-02-28 16:13:40,846 nipype.workflow:INFO [Node] Running "BigPlot" ("niworkflows.interfaces.plotting.FMRISummary") | |
| 200228-16:14:17,74 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.funcMRIQC.ReportsWorkflow.BigPlot". | |
| 2020-02-28 16:14:17,074 nipype.workflow:INFO [Node] Finished "workflow_enumerator.funcMRIQC.ReportsWorkflow.BigPlot". | |
| 200228-16:14:18,639 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.funcMRIQC.ReportsWorkflow.MergePlots" in "/gpfs/scratchfs1/jac18015/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". | |
| 2020-02-28 16:14:18,639 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.funcMRIQC.ReportsWorkflow.MergePlots" in "/gpfs/scratchfs1/jac18015/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". | |
| 200228-16:14:18,642 nipype.workflow INFO: | |
| [Node] Running "MergePlots" ("nipype.interfaces.utility.base.Merge") | |
| 2020-02-28 16:14:18,642 nipype.workflow:INFO [Node] Running "MergePlots" ("nipype.interfaces.utility.base.Merge") | |
| 200228-16:14:18,645 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.funcMRIQC.ReportsWorkflow.MergePlots". | |
| 2020-02-28 16:14:18,645 nipype.workflow:INFO [Node] Finished "workflow_enumerator.funcMRIQC.ReportsWorkflow.MergePlots". | |
| 200228-16:14:20,693 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.funcMRIQC.ReportsWorkflow.GenerateReport" in "/gpfs/scratchfs1/jac18015/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". | |
| 2020-02-28 16:14:20,693 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.funcMRIQC.ReportsWorkflow.GenerateReport" in "/gpfs/scratchfs1/jac18015/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". | |
| 200228-16:14:20,724 nipype.workflow INFO: | |
| [Node] Running "GenerateReport" ("nipype.interfaces.utility.wrappers.Function") | |
| 2020-02-28 16:14:20,724 nipype.workflow:INFO [Node] Running "GenerateReport" ("nipype.interfaces.utility.wrappers.Function") | |
| 2020-02-28 16:14:20,962 mriqc.report:WARNING Building bold report: no exclude index was found | |
| 200228-16:14:21,219 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.funcMRIQC.ReportsWorkflow.GenerateReport". | |
| 2020-02-28 16:14:21,219 nipype.workflow:INFO [Node] Finished "workflow_enumerator.funcMRIQC.ReportsWorkflow.GenerateReport". | |
| 200228-16:14:23,188 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.ComputeIQMs.metadata" in "/gpfs/scratchfs1/jac18015/hw3/work/workflow_enumerator/anatMRIQCT2w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/metadata". | |
| 2020-02-28 16:14:23,188 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.ComputeIQMs.metadata" in "/gpfs/scratchfs1/jac18015/hw3/work/workflow_enumerator/anatMRIQCT2w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/metadata". | |
| 200228-16:14:23,227 nipype.workflow INFO: | |
| [Node] Running "metadata" ("niworkflows.interfaces.bids.ReadSidecarJSON") | |
| 2020-02-28 16:14:23,227 nipype.workflow:INFO [Node] Running "metadata" ("niworkflows.interfaces.bids.ReadSidecarJSON") | |
| 200228-16:14:23,659 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT2w.ComputeIQMs.metadata". | |
| 2020-02-28 16:14:23,659 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT2w.ComputeIQMs.metadata". | |
| 200228-16:14:24,752 nipype.workflow INFO: | |
| [Node] Setting-up "_MNItpms2t10" in "/gpfs/scratchfs1/jac18015/hw3/work/workflow_enumerator/anatMRIQCT1w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/MNItpms2t1/mapflow/_MNItpms2t10". | |
| 2020-02-28 16:14:24,752 nipype.workflow:INFO [Node] Setting-up "_MNItpms2t10" in "/gpfs/scratchfs1/jac18015/hw3/work/workflow_enumerator/anatMRIQCT1w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/MNItpms2t1/mapflow/_MNItpms2t10". | |
| 200228-16:14:24,761 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/jac18015/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/jac18015/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 | |
| 2020-02-28 16:14:24,761 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/jac18015/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/jac18015/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 | |
| 200228-16:14:41,599 nipype.workflow INFO: | |
| [Node] Finished "_MNItpms2t10". | |
| 2020-02-28 16:14:41,599 nipype.workflow:INFO [Node] Finished "_MNItpms2t10". | |
| 200228-16:14:42,643 nipype.workflow INFO: | |
| [Node] Setting-up "_MNItpms2t11" in "/gpfs/scratchfs1/jac18015/hw3/work/workflow_enumerator/anatMRIQCT1w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/MNItpms2t1/mapflow/_MNItpms2t11". | |
| 2020-02-28 16:14:42,643 nipype.workflow:INFO [Node] Setting-up "_MNItpms2t11" in "/gpfs/scratchfs1/jac18015/hw3/work/workflow_enumerator/anatMRIQCT1w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/MNItpms2t1/mapflow/_MNItpms2t11". | |
| 200228-16:14:42,646 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/jac18015/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/jac18015/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 | |
| 2020-02-28 16:14:42,646 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/jac18015/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/jac18015/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 | |
| 200228-16:14:59,535 nipype.workflow INFO: | |
| [Node] Finished "_MNItpms2t11". | |
| 2020-02-28 16:14:59,535 nipype.workflow:INFO [Node] Finished "_MNItpms2t11". | |
| 200228-16:15:00,653 nipype.workflow INFO: | |
| [Node] Setting-up "_MNItpms2t12" in "/gpfs/scratchfs1/jac18015/hw3/work/workflow_enumerator/anatMRIQCT1w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/MNItpms2t1/mapflow/_MNItpms2t12". | |
| 2020-02-28 16:15:00,653 nipype.workflow:INFO [Node] Setting-up "_MNItpms2t12" in "/gpfs/scratchfs1/jac18015/hw3/work/workflow_enumerator/anatMRIQCT1w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/MNItpms2t1/mapflow/_MNItpms2t12". | |
| 200228-16:15:00,656 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/jac18015/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/jac18015/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 | |
| 2020-02-28 16:15:00,656 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/jac18015/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/jac18015/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 | |
| 200228-16:15:17,490 nipype.workflow INFO: | |
| [Node] Finished "_MNItpms2t12". | |
| 2020-02-28 16:15:17,490 nipype.workflow:INFO [Node] Finished "_MNItpms2t12". | |
| 200228-16:15:18,678 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.ComputeIQMs.MNItpms2t1" in "/gpfs/scratchfs1/jac18015/hw3/work/workflow_enumerator/anatMRIQCT1w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/MNItpms2t1". | |
| 2020-02-28 16:15:18,678 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.ComputeIQMs.MNItpms2t1" in "/gpfs/scratchfs1/jac18015/hw3/work/workflow_enumerator/anatMRIQCT1w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/MNItpms2t1". | |
| 200228-16:15:18,750 nipype.workflow INFO: | |
| [Node] Setting-up "_MNItpms2t10" in "/gpfs/scratchfs1/jac18015/hw3/work/workflow_enumerator/anatMRIQCT1w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/MNItpms2t1/mapflow/_MNItpms2t10". | |
| 2020-02-28 16:15:18,750 nipype.workflow:INFO [Node] Setting-up "_MNItpms2t10" in "/gpfs/scratchfs1/jac18015/hw3/work/workflow_enumerator/anatMRIQCT1w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/MNItpms2t1/mapflow/_MNItpms2t10". | |
| 200228-16:15:18,752 nipype.workflow INFO: | |
| [Node] Cached "_MNItpms2t10" - collecting precomputed outputs | |
| 2020-02-28 16:15:18,752 nipype.workflow:INFO [Node] Cached "_MNItpms2t10" - collecting precomputed outputs | |
| 200228-16:15:18,752 nipype.workflow INFO: | |
| [Node] "_MNItpms2t10" found cached. | |
| 2020-02-28 16:15:18,752 nipype.workflow:INFO [Node] "_MNItpms2t10" found cached. | |
| 200228-16:15:18,753 nipype.workflow INFO: | |
| [Node] Setting-up "_MNItpms2t11" in "/gpfs/scratchfs1/jac18015/hw3/work/workflow_enumerator/anatMRIQCT1w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/MNItpms2t1/mapflow/_MNItpms2t11". | |
| 2020-02-28 16:15:18,753 nipype.workflow:INFO [Node] Setting-up "_MNItpms2t11" in "/gpfs/scratchfs1/jac18015/hw3/work/workflow_enumerator/anatMRIQCT1w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/MNItpms2t1/mapflow/_MNItpms2t11". | |
| 200228-16:15:18,754 nipype.workflow INFO: | |
| [Node] Cached "_MNItpms2t11" - collecting precomputed outputs | |
| 2020-02-28 16:15:18,754 nipype.workflow:INFO [Node] Cached "_MNItpms2t11" - collecting precomputed outputs | |
| 200228-16:15:18,754 nipype.workflow INFO: | |
| [Node] "_MNItpms2t11" found cached. | |
| 2020-02-28 16:15:18,754 nipype.workflow:INFO [Node] "_MNItpms2t11" found cached. | |
| 200228-16:15:18,755 nipype.workflow INFO: | |
| [Node] Setting-up "_MNItpms2t12" in "/gpfs/scratchfs1/jac18015/hw3/work/workflow_enumerator/anatMRIQCT1w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/MNItpms2t1/mapflow/_MNItpms2t12". | |
| 2020-02-28 16:15:18,755 nipype.workflow:INFO [Node] Setting-up "_MNItpms2t12" in "/gpfs/scratchfs1/jac18015/hw3/work/workflow_enumerator/anatMRIQCT1w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/MNItpms2t1/mapflow/_MNItpms2t12". | |
| 200228-16:15:18,755 nipype.workflow INFO: | |
| [Node] Cached "_MNItpms2t12" - collecting precomputed outputs | |
| 2020-02-28 16:15:18,755 nipype.workflow:INFO [Node] Cached "_MNItpms2t12" - collecting precomputed outputs | |
| 200228-16:15:18,756 nipype.workflow INFO: | |
| [Node] "_MNItpms2t12" found cached. | |
| 2020-02-28 16:15:18,756 nipype.workflow:INFO [Node] "_MNItpms2t12" found cached. | |
| 200228-16:15:18,769 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT1w.ComputeIQMs.MNItpms2t1". | |
| 2020-02-28 16:15:18,769 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT1w.ComputeIQMs.MNItpms2t1". | |
| 200228-16:15:20,798 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.ComputeIQMs.measures" in "/gpfs/scratchfs1/jac18015/hw3/work/workflow_enumerator/anatMRIQCT1w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/measures". | |
| 2020-02-28 16:15:20,798 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.ComputeIQMs.measures" in "/gpfs/scratchfs1/jac18015/hw3/work/workflow_enumerator/anatMRIQCT1w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/measures". | |
| 200228-16:15:20,803 nipype.workflow INFO: | |
| [Node] Running "measures" ("mriqc.interfaces.anatomical.StructuralQC") | |
| 2020-02-28 16:15:20,803 nipype.workflow:INFO [Node] Running "measures" ("mriqc.interfaces.anatomical.StructuralQC") | |
| 200228-16:16:00,778 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT1w.ComputeIQMs.measures". | |
| 2020-02-28 16:16:00,778 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT1w.ComputeIQMs.measures". | |
| 200228-16:16:04,879 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.ReportsWorkflow.GenerateReport" in "/gpfs/scratchfs1/jac18015/hw3/work/workflow_enumerator/anatMRIQCT1w/ReportsWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/GenerateReport". | |
| 2020-02-28 16:16:04,879 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.ReportsWorkflow.GenerateReport" in "/gpfs/scratchfs1/jac18015/hw3/work/workflow_enumerator/anatMRIQCT1w/ReportsWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/GenerateReport". | |
| 200228-16:16:04,897 nipype.workflow INFO: | |
| [Node] Running "GenerateReport" ("nipype.interfaces.utility.wrappers.Function") | |
| 2020-02-28 16:16:04,897 nipype.workflow:INFO [Node] Running "GenerateReport" ("nipype.interfaces.utility.wrappers.Function") | |
| 200228-16:16:05,249 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT1w.ReportsWorkflow.GenerateReport". | |
| 2020-02-28 16:16:05,249 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT1w.ReportsWorkflow.GenerateReport". | |
| 200228-16:16:07,278 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.UploadMetrics" in "/gpfs/scratchfs1/jac18015/hw3/work/workflow_enumerator/anatMRIQCT1w/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/UploadMetrics". | |
| 2020-02-28 16:16:07,278 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.UploadMetrics" in "/gpfs/scratchfs1/jac18015/hw3/work/workflow_enumerator/anatMRIQCT1w/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/UploadMetrics". | |
| 200228-16:16:07,284 nipype.workflow INFO: | |
| [Node] Running "UploadMetrics" ("mriqc.interfaces.webapi.UploadIQMs") | |
| 2020-02-28 16:16:07,284 nipype.workflow:INFO [Node] Running "UploadMetrics" ("mriqc.interfaces.webapi.UploadIQMs") | |
| 200228-16:16:08,347 nipype.interface INFO: | |
| MRIQC Web API: submitting to <https://mriqc.nimh.nih.gov:443/api/v1/T1w> | |
| 2020-02-28 16:16:08,347 nipype.interface:INFO MRIQC Web API: submitting to <https://mriqc.nimh.nih.gov:443/api/v1/T1w> | |
| 200228-16:16:08,510 nipype.interface INFO: | |
| QC metrics successfully uploaded. | |
| 2020-02-28 16:16:08,510 nipype.interface:INFO QC metrics successfully uploaded. | |
| 200228-16:16:08,513 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT1w.UploadMetrics". | |
| 2020-02-28 16:16:08,513 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT1w.UploadMetrics". | |
| 2020-02-28 16:16:12,363 niworkflows:INFO Terminal outputs of initialization saved (/gpfs/scratchfs1/jac18015/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). | |
| 2020-02-28 16:16:12,363 niworkflows:INFO Loading settings from file /usr/local/miniconda/lib/python3.7/site-packages/niworkflows/data/t1w-mni_registration_fast_000.json. | |
| 2020-02-28 16:16:12,388 niworkflows:INFO Retry #1, commandline: | |
| antsRegistration --collapse-output-transforms 1 --dimensionality 3 --float 0 --initial-moving-transform [ /gpfs/scratchfs1/jac18015/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/jac18015/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/jac18015/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/jac18015/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/jac18015/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/jac18015/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/jac18015/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 | |
| 200228-16:17:32,937 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT2w.segmentation". | |
| 2020-02-28 16:17:32,937 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT2w.segmentation". | |
| 200228-16:17:34,711 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.ComputeIQMs.harmonize" in "/gpfs/scratchfs1/jac18015/hw3/work/workflow_enumerator/anatMRIQCT2w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/harmonize". | |
| 2020-02-28 16:17:34,711 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.ComputeIQMs.harmonize" in "/gpfs/scratchfs1/jac18015/hw3/work/workflow_enumerator/anatMRIQCT2w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/harmonize". | |
| 200228-16:17:34,713 nipype.workflow INFO: | |
| [Node] Running "harmonize" ("mriqc.interfaces.anatomical.Harmonize") | |
| 2020-02-28 16:17:34,713 nipype.workflow:INFO [Node] Running "harmonize" ("mriqc.interfaces.anatomical.Harmonize") | |
| 200228-16:17:44,969 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT2w.ComputeIQMs.harmonize". | |
| 2020-02-28 16:17:44,969 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT2w.ComputeIQMs.harmonize". | |
| 2020-02-28 16:20:58,561 niworkflows:INFO Successful spatial normalization (retry #1). | |
| 2020-02-28 16:21:02,116 niworkflows:INFO Report - setting fixed (/gpfs/scratchfs1/jac18015/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/jac18015/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 | |
| 2020-02-28 16:21:02,116 niworkflows:INFO Generating visual report | |
| 200228-16:21:11,524 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT2w.SpatialNormalization.SpatialNormalization". | |
| 2020-02-28 16:21:11,524 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT2w.SpatialNormalization.SpatialNormalization". | |
| 200228-16:21:12,772 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.AirMaskWorkflow.invert_xfm" in "/gpfs/scratchfs1/jac18015/hw3/work/workflow_enumerator/anatMRIQCT2w/AirMaskWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/invert_xfm". | |
| 2020-02-28 16:21:12,772 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.AirMaskWorkflow.invert_xfm" in "/gpfs/scratchfs1/jac18015/hw3/work/workflow_enumerator/anatMRIQCT2w/AirMaskWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/invert_xfm". | |
| 200228-16:21:12,792 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/jac18015/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/jac18015/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 | |
| 2020-02-28 16:21:12,792 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/jac18015/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/jac18015/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 | |
| 200228-16:21:14,819 nipype.workflow INFO: | |
| [Node] Setting-up "_MNItpms2t10" in "/gpfs/scratchfs1/jac18015/hw3/work/workflow_enumerator/anatMRIQCT2w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/MNItpms2t1/mapflow/_MNItpms2t10". | |
| 2020-02-28 16:21:14,819 nipype.workflow:INFO [Node] Setting-up "_MNItpms2t10" in "/gpfs/scratchfs1/jac18015/hw3/work/workflow_enumerator/anatMRIQCT2w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/MNItpms2t1/mapflow/_MNItpms2t10". | |
| 200228-16:21:14,821 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/jac18015/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/jac18015/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 | |
| 2020-02-28 16:21:14,821 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/jac18015/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/jac18015/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 | |
| 200228-16:21:14,832 nipype.workflow INFO: | |
| [Node] Setting-up "_MNItpms2t11" in "/gpfs/scratchfs1/jac18015/hw3/work/workflow_enumerator/anatMRIQCT2w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/MNItpms2t1/mapflow/_MNItpms2t11". | |
| 2020-02-28 16:21:14,832 nipype.workflow:INFO [Node] Setting-up "_MNItpms2t11" in "/gpfs/scratchfs1/jac18015/hw3/work/workflow_enumerator/anatMRIQCT2w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/MNItpms2t1/mapflow/_MNItpms2t11". | |
| 200228-16:21:14,846 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/jac18015/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/jac18015/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 | |
| 2020-02-28 16:21:14,846 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/jac18015/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/jac18015/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 | |
| 200228-16:21:31,452 nipype.workflow INFO: | |
| [Node] Finished "_MNItpms2t10". | |
| 2020-02-28 16:21:31,452 nipype.workflow:INFO [Node] Finished "_MNItpms2t10". | |
| 200228-16:21:31,590 nipype.workflow INFO: | |
| [Node] Finished "_MNItpms2t11". | |
| 2020-02-28 16:21:31,590 nipype.workflow:INFO [Node] Finished "_MNItpms2t11". | |
| 200228-16:21:32,837 nipype.workflow INFO: | |
| [Node] Setting-up "_MNItpms2t12" in "/gpfs/scratchfs1/jac18015/hw3/work/workflow_enumerator/anatMRIQCT2w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/MNItpms2t1/mapflow/_MNItpms2t12". | |
| 2020-02-28 16:21:32,837 nipype.workflow:INFO [Node] Setting-up "_MNItpms2t12" in "/gpfs/scratchfs1/jac18015/hw3/work/workflow_enumerator/anatMRIQCT2w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/MNItpms2t1/mapflow/_MNItpms2t12". | |
| 200228-16:21:32,840 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/jac18015/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/jac18015/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 | |
| 2020-02-28 16:21:32,840 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/jac18015/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/jac18015/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 | |
| 200228-16:21:44,473 nipype.workflow INFO: | |
| [Node] Finished "_MNItpms2t12". | |
| 2020-02-28 16:21:44,473 nipype.workflow:INFO [Node] Finished "_MNItpms2t12". | |
| 200228-16:21:44,844 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.ComputeIQMs.MNItpms2t1" in "/gpfs/scratchfs1/jac18015/hw3/work/workflow_enumerator/anatMRIQCT2w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/MNItpms2t1". | |
| 2020-02-28 16:21:44,844 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.ComputeIQMs.MNItpms2t1" in "/gpfs/scratchfs1/jac18015/hw3/work/workflow_enumerator/anatMRIQCT2w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/MNItpms2t1". | |
| 200228-16:21:44,855 nipype.workflow INFO: | |
| [Node] Setting-up "_MNItpms2t10" in "/gpfs/scratchfs1/jac18015/hw3/work/workflow_enumerator/anatMRIQCT2w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/MNItpms2t1/mapflow/_MNItpms2t10". | |
| 2020-02-28 16:21:44,855 nipype.workflow:INFO [Node] Setting-up "_MNItpms2t10" in "/gpfs/scratchfs1/jac18015/hw3/work/workflow_enumerator/anatMRIQCT2w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/MNItpms2t1/mapflow/_MNItpms2t10". | |
| 200228-16:21:44,856 nipype.workflow INFO: | |
| [Node] Cached "_MNItpms2t10" - collecting precomputed outputs | |
| 2020-02-28 16:21:44,856 nipype.workflow:INFO [Node] Cached "_MNItpms2t10" - collecting precomputed outputs | |
| 200228-16:21:44,856 nipype.workflow INFO: | |
| [Node] "_MNItpms2t10" found cached. | |
| 2020-02-28 16:21:44,856 nipype.workflow:INFO [Node] "_MNItpms2t10" found cached. | |
| 200228-16:21:44,857 nipype.workflow INFO: | |
| [Node] Setting-up "_MNItpms2t11" in "/gpfs/scratchfs1/jac18015/hw3/work/workflow_enumerator/anatMRIQCT2w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/MNItpms2t1/mapflow/_MNItpms2t11". | |
| 2020-02-28 16:21:44,857 nipype.workflow:INFO [Node] Setting-up "_MNItpms2t11" in "/gpfs/scratchfs1/jac18015/hw3/work/workflow_enumerator/anatMRIQCT2w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/MNItpms2t1/mapflow/_MNItpms2t11". | |
| 200228-16:21:44,858 nipype.workflow INFO: | |
| [Node] Cached "_MNItpms2t11" - collecting precomputed outputs | |
| 2020-02-28 16:21:44,858 nipype.workflow:INFO [Node] Cached "_MNItpms2t11" - collecting precomputed outputs | |
| 200228-16:21:44,858 nipype.workflow INFO: | |
| [Node] "_MNItpms2t11" found cached. | |
| 2020-02-28 16:21:44,858 nipype.workflow:INFO [Node] "_MNItpms2t11" found cached. | |
| 200228-16:21:44,859 nipype.workflow INFO: | |
| [Node] Setting-up "_MNItpms2t12" in "/gpfs/scratchfs1/jac18015/hw3/work/workflow_enumerator/anatMRIQCT2w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/MNItpms2t1/mapflow/_MNItpms2t12". | |
| 2020-02-28 16:21:44,859 nipype.workflow:INFO [Node] Setting-up "_MNItpms2t12" in "/gpfs/scratchfs1/jac18015/hw3/work/workflow_enumerator/anatMRIQCT2w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/MNItpms2t1/mapflow/_MNItpms2t12". | |
| 200228-16:21:44,859 nipype.workflow INFO: | |
| [Node] Cached "_MNItpms2t12" - collecting precomputed outputs | |
| 2020-02-28 16:21:44,859 nipype.workflow:INFO [Node] Cached "_MNItpms2t12" - collecting precomputed outputs | |
| 200228-16:21:44,859 nipype.workflow INFO: | |
| [Node] "_MNItpms2t12" found cached. | |
| 2020-02-28 16:21:44,859 nipype.workflow:INFO [Node] "_MNItpms2t12" found cached. | |
| 200228-16:21:44,872 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT2w.ComputeIQMs.MNItpms2t1". | |
| 2020-02-28 16:21:44,872 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT2w.ComputeIQMs.MNItpms2t1". | |
| 200228-16:26:06,433 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT2w.AirMaskWorkflow.invert_xfm". | |
| 2020-02-28 16:26:06,433 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT2w.AirMaskWorkflow.invert_xfm". | |
| 200228-16:26:06,916 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.AirMaskWorkflow.ArtifactMask" in "/gpfs/scratchfs1/jac18015/hw3/work/workflow_enumerator/anatMRIQCT2w/AirMaskWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/ArtifactMask". | |
| 2020-02-28 16:26:06,916 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.AirMaskWorkflow.ArtifactMask" in "/gpfs/scratchfs1/jac18015/hw3/work/workflow_enumerator/anatMRIQCT2w/AirMaskWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/ArtifactMask". | |
| 200228-16:26:06,919 nipype.workflow INFO: | |
| [Node] Running "ArtifactMask" ("mriqc.interfaces.anatomical.ArtifactMask") | |
| 2020-02-28 16:26:06,919 nipype.workflow:INFO [Node] Running "ArtifactMask" ("mriqc.interfaces.anatomical.ArtifactMask") | |
| 200228-16:26:13,632 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT2w.AirMaskWorkflow.ArtifactMask". | |
| 2020-02-28 16:26:13,632 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT2w.AirMaskWorkflow.ArtifactMask". | |
| 200228-16:26:14,909 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.ComputeIQMs.ComputeQI2" in "/gpfs/scratchfs1/jac18015/hw3/work/workflow_enumerator/anatMRIQCT2w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/ComputeQI2". | |
| 2020-02-28 16:26:14,909 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.ComputeIQMs.ComputeQI2" in "/gpfs/scratchfs1/jac18015/hw3/work/workflow_enumerator/anatMRIQCT2w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/ComputeQI2". | |
| 200228-16:26:14,911 nipype.workflow INFO: | |
| [Node] Running "ComputeQI2" ("mriqc.interfaces.anatomical.ComputeQI2") | |
| 2020-02-28 16:26:14,911 nipype.workflow:INFO [Node] Running "ComputeQI2" ("mriqc.interfaces.anatomical.ComputeQI2") | |
| 200228-16:26:14,936 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.ComputeIQMs.measures" in "/gpfs/scratchfs1/jac18015/hw3/work/workflow_enumerator/anatMRIQCT2w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/measures". | |
| 2020-02-28 16:26:14,936 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.ComputeIQMs.measures" in "/gpfs/scratchfs1/jac18015/hw3/work/workflow_enumerator/anatMRIQCT2w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/measures". | |
| 200228-16:26:14,938 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.ComputeIQMs.provenance" in "/gpfs/scratchfs1/jac18015/hw3/work/workflow_enumerator/anatMRIQCT2w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/provenance". | |
| 2020-02-28 16:26:14,938 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.ComputeIQMs.provenance" in "/gpfs/scratchfs1/jac18015/hw3/work/workflow_enumerator/anatMRIQCT2w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/provenance". | |
| 200228-16:26:14,941 nipype.workflow INFO: | |
| [Node] Running "measures" ("mriqc.interfaces.anatomical.StructuralQC") | |
| 2020-02-28 16:26:14,941 nipype.workflow:INFO [Node] Running "measures" ("mriqc.interfaces.anatomical.StructuralQC") | |
| 200228-16:26:14,948 nipype.workflow INFO: | |
| [Node] Running "provenance" ("nipype.interfaces.utility.wrappers.Function") | |
| 2020-02-28 16:26:14,948 nipype.workflow:INFO [Node] Running "provenance" ("nipype.interfaces.utility.wrappers.Function") | |
| 200228-16:26:15,459 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT2w.ComputeIQMs.provenance". | |
| 2020-02-28 16:26:15,459 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT2w.ComputeIQMs.provenance". | |
| 200228-16:26:40,485 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT2w.ComputeIQMs.measures". | |
| 2020-02-28 16:26:40,485 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT2w.ComputeIQMs.measures". | |
| 200228-16:27:15,360 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT2w.ComputeIQMs.ComputeQI2". | |
| 2020-02-28 16:27:15,360 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT2w.ComputeIQMs.ComputeQI2". | |
| 200228-16:27:18,974 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.ReportsWorkflow.GenerateReport" in "/gpfs/scratchfs1/jac18015/hw3/work/workflow_enumerator/anatMRIQCT2w/ReportsWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/GenerateReport". | |
| 2020-02-28 16:27:18,974 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.ReportsWorkflow.GenerateReport" in "/gpfs/scratchfs1/jac18015/hw3/work/workflow_enumerator/anatMRIQCT2w/ReportsWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/GenerateReport". | |
| 200228-16:27:18,977 nipype.workflow INFO: | |
| [Node] Running "GenerateReport" ("nipype.interfaces.utility.wrappers.Function") | |
| 2020-02-28 16:27:18,977 nipype.workflow:INFO [Node] Running "GenerateReport" ("nipype.interfaces.utility.wrappers.Function") | |
| 200228-16:27:18,979 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.UploadMetrics" in "/gpfs/scratchfs1/jac18015/hw3/work/workflow_enumerator/anatMRIQCT2w/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/UploadMetrics". | |
| 2020-02-28 16:27:18,979 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.UploadMetrics" in "/gpfs/scratchfs1/jac18015/hw3/work/workflow_enumerator/anatMRIQCT2w/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/UploadMetrics". | |
| 200228-16:27:18,986 nipype.workflow INFO: | |
| [Node] Running "UploadMetrics" ("mriqc.interfaces.webapi.UploadIQMs") | |
| 2020-02-28 16:27:18,986 nipype.workflow:INFO [Node] Running "UploadMetrics" ("mriqc.interfaces.webapi.UploadIQMs") | |
| 200228-16:27:19,197 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT2w.ReportsWorkflow.GenerateReport". | |
| 2020-02-28 16:27:19,197 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT2w.ReportsWorkflow.GenerateReport". | |
| 200228-16:27:19,391 nipype.interface INFO: | |
| MRIQC Web API: submitting to <https://mriqc.nimh.nih.gov:443/api/v1/T2w> | |
| 2020-02-28 16:27:19,391 nipype.interface:INFO MRIQC Web API: submitting to <https://mriqc.nimh.nih.gov:443/api/v1/T2w> | |
| 200228-16:27:19,522 nipype.interface INFO: | |
| QC metrics successfully uploaded. | |
| 2020-02-28 16:27:19,522 nipype.interface:INFO QC metrics successfully uploaded. | |
| 200228-16:27:19,525 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT2w.UploadMetrics". | |
| 2020-02-28 16:27:19,525 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT2w.UploadMetrics". | |
| 2020-02-28 16:27:22,939 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. | |
| 2020-02-28 16:27:23,097 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(), | |
| 2020-02-28 16:27:23,099 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(), | |
| 2020-02-28 16:27:23,099 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() | |