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| 2020-02-28 13:59:28,850 mriqc:IMPORTANT | |
| Running MRIQC version 0.15.0: | |
| * BIDS dataset path: /data. | |
| * Output folder: /out. | |
| * Analysis levels: group, participant. | |
| 2020-02-28 13:59:33,617 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 13:59:34,190 py.warnings:WARNING /usr/local/miniconda/lib/python3.7/site-packages/sklearn/metrics/classification.py:349: DeprecationWarning: invalid escape sequence \k | |
| """ | |
| 2020-02-28 13:59:34,194 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 13:59:35,882 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 13:59:36,981 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 13:59:38,052 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 13:59:38,145 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 13:59:38,158 py.warnings:WARNING /usr/local/miniconda/lib/python3.7/site-packages/sklearn/datasets/samples_generator.py:839: DeprecationWarning: invalid escape sequence \# | |
| """ | |
| 2020-02-28 13:59:38,158 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 13:59:38,192 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 13:59:38,250 py.warnings:WARNING /usr/local/miniconda/lib/python3.7/site-packages/sklearn/decomposition/nmf.py:972: DeprecationWarning: invalid escape sequence \s | |
| """ | |
| 2020-02-28 13:59:38,324 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 13:59:38,491 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 13:59:38,646 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 13:59:39,125 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 13:59:39,165 py.warnings:WARNING /usr/local/miniconda/lib/python3.7/site-packages/networkx/generators/geometric.py:275: DeprecationWarning: invalid escape sequence \l | |
| """ | |
| 2020-02-28 13:59:39,200 py.warnings:WARNING /usr/local/miniconda/lib/python3.7/site-packages/networkx/algorithms/cluster.py:537: DeprecationWarning: invalid escape sequence \m | |
| """ | |
| 2020-02-28 13:59:39,279 py.warnings:WARNING /usr/local/miniconda/lib/python3.7/site-packages/networkx/algorithms/reciprocity.py:47: DeprecationWarning: invalid escape sequence \i | |
| """ | |
| 2020-02-28 13:59:39,287 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 13:59:39,408 py.warnings:WARNING /usr/local/miniconda/lib/python3.7/site-packages/networkx/generators/line.py:113: DeprecationWarning: invalid escape sequence \{ | |
| """ | |
| 2020-02-28 13:59:39,474 py.warnings:WARNING /usr/local/miniconda/lib/python3.7/site-packages/networkx/linalg/modularitymatrix.py:74: DeprecationWarning: invalid escape sequence \o | |
| """ | |
| 200228-13:59:40,228 nipype.workflow INFO: | |
| Building anatomical MRIQC workflow, datasets list: ['sub-01/ses-01/anat/sub-01_ses-01_T1w.nii.gz'] | |
| 2020-02-28 13:59:40,228 nipype.workflow:INFO Building anatomical MRIQC workflow, datasets list: ['sub-01/ses-01/anat/sub-01_ses-01_T1w.nii.gz'] | |
| 200228-13:59:40,467 nipype.workflow INFO: | |
| Building anatomical MRIQC workflow, datasets list: ['sub-01/ses-01/anat/sub-01_ses-01_T2w.nii.gz'] | |
| 2020-02-28 13:59:40,467 nipype.workflow:INFO Building anatomical MRIQC workflow, datasets list: ['sub-01/ses-01/anat/sub-01_ses-01_T2w.nii.gz'] | |
| 2020-02-28 13:59:49,427 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 13:59:49,466 py.warnings:WARNING /usr/local/miniconda/lib/python3.7/site-packages/sklearn/metrics/classification.py:349: DeprecationWarning: invalid escape sequence \k | |
| """ | |
| 2020-02-28 13:59:49,469 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 13:59:49,549 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 13:59:49,549 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 13:59:49,693 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 13:59:49,703 py.warnings:WARNING /usr/local/miniconda/lib/python3.7/site-packages/sklearn/datasets/samples_generator.py:839: DeprecationWarning: invalid escape sequence \# | |
| """ | |
| 2020-02-28 13:59:49,703 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 13:59:49,729 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 13:59:49,770 py.warnings:WARNING /usr/local/miniconda/lib/python3.7/site-packages/sklearn/decomposition/nmf.py:972: DeprecationWarning: invalid escape sequence \s | |
| """ | |
| 2020-02-28 13:59:49,817 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 13:59:50,014 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 13:59:50,014 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 13:59:50,028 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 13:59:50,035 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 13:59:50,035 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 13:59:50,166 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 13:59:50,753 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 13:59:52,753 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) | |
| 200228-13:59:53,613 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.funcMRIQC.non_steady_state_detector" in "/gpfs/scratchfs1/ham19006/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". | |
| 200228-13:59:53,615 nipype.workflow INFO: | |
| [Node] Running "non_steady_state_detector" ("nipype.algorithms.confounds.NonSteadyStateDetector") | |
| 200228-13:59:56,684 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.conform" in "/gpfs/scratchfs1/ham19006/hw3/work/workflow_enumerator/anatMRIQCT1w/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/conform". | |
| 2020-02-28 13:59:56,684 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.conform" in "/gpfs/scratchfs1/ham19006/hw3/work/workflow_enumerator/anatMRIQCT1w/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/conform". | |
| 200228-13:59:56,686 nipype.workflow INFO: | |
| [Node] Running "conform" ("mriqc.interfaces.common.ConformImage") | |
| 2020-02-28 13:59:56,686 nipype.workflow:INFO [Node] Running "conform" ("mriqc.interfaces.common.ConformImage") | |
| 200228-13:59:57,676 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.ComputeIQMs.metadata" in "/gpfs/scratchfs1/ham19006/hw3/work/workflow_enumerator/anatMRIQCT1w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/metadata". | |
| 200228-13:59:57,690 nipype.workflow INFO: | |
| [Node] Running "metadata" ("niworkflows.interfaces.bids.ReadSidecarJSON") | |
| 200228-13:59:57,732 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT1w.ComputeIQMs.metadata". | |
| 200228-13:59:58,112 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.funcMRIQC.non_steady_state_detector". | |
| 200228-13:59:58,245 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT1w.conform". | |
| 2020-02-28 13:59:58,245 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT1w.conform". | |
| 200228-13:59:58,832 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.funcMRIQC.sanitize" in "/gpfs/scratchfs1/ham19006/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". | |
| 200228-13:59:58,834 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.AirMaskWorkflow.RotationMask" in "/gpfs/scratchfs1/ham19006/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 13:59:58,834 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.AirMaskWorkflow.RotationMask" in "/gpfs/scratchfs1/ham19006/hw3/work/workflow_enumerator/anatMRIQCT1w/AirMaskWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/RotationMask". | |
| 200228-13:59:58,834 nipype.workflow INFO: | |
| [Node] Running "sanitize" ("niworkflows.interfaces.utils.SanitizeImage") | |
| 200228-13:59:58,836 nipype.workflow INFO: | |
| [Node] Running "RotationMask" ("mriqc.interfaces.anatomical.RotationMask") | |
| 2020-02-28 13:59:58,836 nipype.workflow:INFO [Node] Running "RotationMask" ("mriqc.interfaces.anatomical.RotationMask") | |
| 200228-14:00:00,624 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.ReportsWorkflow.PlotMosaicNoise" in "/gpfs/scratchfs1/ham19006/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 14:00:00,624 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.ReportsWorkflow.PlotMosaicNoise" in "/gpfs/scratchfs1/ham19006/hw3/work/workflow_enumerator/anatMRIQCT1w/ReportsWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/PlotMosaicNoise". | |
| 200228-14:00:00,626 nipype.workflow INFO: | |
| [Node] Running "PlotMosaicNoise" ("mriqc.interfaces.viz.PlotMosaic") | |
| 2020-02-28 14:00:00,626 nipype.workflow:INFO [Node] Running "PlotMosaicNoise" ("mriqc.interfaces.viz.PlotMosaic") | |
| 200228-14:00:00,737 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT1w.AirMaskWorkflow.RotationMask". | |
| 2020-02-28 14:00:00,737 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT1w.AirMaskWorkflow.RotationMask". | |
| 200228-14:00:00,833 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.AFNISkullStripWorkflow.inu_n4" in "/gpfs/scratchfs1/ham19006/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 14:00:00,833 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.AFNISkullStripWorkflow.inu_n4" in "/gpfs/scratchfs1/ham19006/hw3/work/workflow_enumerator/anatMRIQCT1w/AFNISkullStripWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/inu_n4". | |
| 200228-14:00:00,836 nipype.workflow INFO: | |
| [Node] Running "inu_n4" ("nipype.interfaces.ants.segmentation.N4BiasFieldCorrection"), a CommandLine Interface with command: | |
| N4BiasFieldCorrection -d 3 --input-image /gpfs/scratchfs1/ham19006/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 14:00:00,836 nipype.workflow:INFO [Node] Running "inu_n4" ("nipype.interfaces.ants.segmentation.N4BiasFieldCorrection"), a CommandLine Interface with command: | |
| N4BiasFieldCorrection -d 3 --input-image /gpfs/scratchfs1/ham19006/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 ] | |
| 200228-14:00:14,714 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT1w.ReportsWorkflow.PlotMosaicNoise". | |
| 2020-02-28 14:00:14,714 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT1w.ReportsWorkflow.PlotMosaicNoise". | |
| 200228-14:00:15,823 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.ComputeIQMs.metadata" in "/gpfs/scratchfs1/ham19006/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 14:00:15,823 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.ComputeIQMs.metadata" in "/gpfs/scratchfs1/ham19006/hw3/work/workflow_enumerator/anatMRIQCT2w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/metadata". | |
| 200228-14:00:15,829 nipype.workflow INFO: | |
| [Node] Running "metadata" ("niworkflows.interfaces.bids.ReadSidecarJSON") | |
| 2020-02-28 14:00:15,829 nipype.workflow:INFO [Node] Running "metadata" ("niworkflows.interfaces.bids.ReadSidecarJSON") | |
| 200228-14:00:15,907 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT2w.ComputeIQMs.metadata". | |
| 2020-02-28 14:00:15,907 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT2w.ComputeIQMs.metadata". | |
| 200228-14:00:16,849 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.conform" in "/gpfs/scratchfs1/ham19006/hw3/work/workflow_enumerator/anatMRIQCT2w/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/conform". | |
| 2020-02-28 14:00:16,849 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.conform" in "/gpfs/scratchfs1/ham19006/hw3/work/workflow_enumerator/anatMRIQCT2w/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/conform". | |
| 200228-14:00:16,857 nipype.workflow INFO: | |
| [Node] Running "conform" ("mriqc.interfaces.common.ConformImage") | |
| 2020-02-28 14:00:16,857 nipype.workflow:INFO [Node] Running "conform" ("mriqc.interfaces.common.ConformImage") | |
| 200228-14:00:18,32 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT2w.conform". | |
| 2020-02-28 14:00:18,032 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT2w.conform". | |
| 200228-14:00:18,852 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.ReportsWorkflow.PlotMosaicNoise" in "/gpfs/scratchfs1/ham19006/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 14:00:18,852 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.ReportsWorkflow.PlotMosaicNoise" in "/gpfs/scratchfs1/ham19006/hw3/work/workflow_enumerator/anatMRIQCT2w/ReportsWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/PlotMosaicNoise". | |
| 200228-14:00:18,857 nipype.workflow INFO: | |
| [Node] Running "PlotMosaicNoise" ("mriqc.interfaces.viz.PlotMosaic") | |
| 2020-02-28 14:00:18,857 nipype.workflow:INFO [Node] Running "PlotMosaicNoise" ("mriqc.interfaces.viz.PlotMosaic") | |
| 200228-14:00:19,46 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.funcMRIQC.sanitize". | |
| 200228-14:00:20,857 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.funcMRIQC.ReportsWorkflow.SpikesMask" in "/gpfs/scratchfs1/ham19006/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". | |
| 200228-14:00:20,860 nipype.workflow INFO: | |
| [Node] Running "SpikesMask" ("nipype.interfaces.utility.wrappers.Function") | |
| 200228-14:00:26,962 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.funcMRIQC.ReportsWorkflow.SpikesMask". | |
| 200228-14:00:28,887 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.funcMRIQC.ReportsWorkflow.SpikesFinderBgMask" in "/gpfs/scratchfs1/ham19006/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 14:00:28,887 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.funcMRIQC.ReportsWorkflow.SpikesFinderBgMask" in "/gpfs/scratchfs1/ham19006/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". | |
| 200228-14:00:28,895 nipype.workflow INFO: | |
| [Node] Running "SpikesFinderBgMask" ("mriqc.interfaces.functional.Spikes") | |
| 2020-02-28 14:00:28,895 nipype.workflow:INFO [Node] Running "SpikesFinderBgMask" ("mriqc.interfaces.functional.Spikes") | |
| 200228-14:00:32,398 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT2w.ReportsWorkflow.PlotMosaicNoise". | |
| 2020-02-28 14:00:32,398 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT2w.ReportsWorkflow.PlotMosaicNoise". | |
| 200228-14:00:32,866 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.funcMRIQC.fMRI_HMC_afni.gen_ref" in "/gpfs/scratchfs1/ham19006/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 14:00:32,866 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.funcMRIQC.fMRI_HMC_afni.gen_ref" in "/gpfs/scratchfs1/ham19006/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". | |
| 200228-14:00:32,874 nipype.workflow INFO: | |
| [Node] Running "gen_ref" ("niworkflows.interfaces.registration.EstimateReferenceImage") | |
| 2020-02-28 14:00:32,874 nipype.workflow:INFO [Node] Running "gen_ref" ("niworkflows.interfaces.registration.EstimateReferenceImage") | |
| 200228-14:00:34,430 nipype.interface INFO: | |
| stderr 2020-02-28T14:00:34.430765:++ 3dvolreg: AFNI version=AFNI_17.3.03 (Nov 9 2017) [64-bit] | |
| 2020-02-28 14:00:34,430 nipype.interface:INFO stderr 2020-02-28T14:00:34.430765:++ 3dvolreg: AFNI version=AFNI_17.3.03 (Nov 9 2017) [64-bit] | |
| 200228-14:00:34,431 nipype.interface INFO: | |
| stderr 2020-02-28T14:00:34.431216:++ Authored by: RW Cox | |
| 2020-02-28 14:00:34,431 nipype.interface:INFO stderr 2020-02-28T14:00:34.431216:++ Authored by: RW Cox | |
| 200228-14:00:34,443 nipype.interface INFO: | |
| stderr 2020-02-28T14:00:34.442983:[7m*+ WARNING:[0m If you are performing spatial transformations on an oblique dset, | |
| 2020-02-28 14:00:34,443 nipype.interface:INFO stderr 2020-02-28T14:00:34.442983:[7m*+ WARNING:[0m If you are performing spatial transformations on an oblique dset, | |
| 200228-14:00:34,443 nipype.interface INFO: | |
| stderr 2020-02-28T14:00:34.442983: such as /gpfs/scratchfs1/ham19006/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 14:00:34,443 nipype.interface:INFO stderr 2020-02-28T14:00:34.442983: such as /gpfs/scratchfs1/ham19006/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, | |
| 200228-14:00:34,443 nipype.interface INFO: | |
| stderr 2020-02-28T14:00:34.442983: or viewing/combining it with volumes of differing obliquity, | |
| 2020-02-28 14:00:34,443 nipype.interface:INFO stderr 2020-02-28T14:00:34.442983: or viewing/combining it with volumes of differing obliquity, | |
| 200228-14:00:34,443 nipype.interface INFO: | |
| stderr 2020-02-28T14:00:34.442983: you should consider running: | |
| 2020-02-28 14:00:34,443 nipype.interface:INFO stderr 2020-02-28T14:00:34.442983: you should consider running: | |
| 200228-14:00:34,443 nipype.interface INFO: | |
| stderr 2020-02-28T14:00:34.442983: 3dWarp -deoblique | |
| 2020-02-28 14:00:34,443 nipype.interface:INFO stderr 2020-02-28T14:00:34.442983: 3dWarp -deoblique | |
| 200228-14:00:34,443 nipype.interface INFO: | |
| stderr 2020-02-28T14:00:34.442983: on this and other oblique datasets in the same session. | |
| 2020-02-28 14:00:34,443 nipype.interface:INFO stderr 2020-02-28T14:00:34.442983: on this and other oblique datasets in the same session. | |
| 200228-14:00:34,443 nipype.interface INFO: | |
| stderr 2020-02-28T14:00:34.442983: See 3dWarp -help for details. | |
| 2020-02-28 14:00:34,443 nipype.interface:INFO stderr 2020-02-28T14:00:34.442983: See 3dWarp -help for details. | |
| 200228-14:00:34,443 nipype.interface INFO: | |
| stderr 2020-02-28T14:00:34.443658:++ Oblique dataset:/gpfs/scratchfs1/ham19006/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 14:00:34,443 nipype.interface:INFO stderr 2020-02-28T14:00:34.443658:++ Oblique dataset:/gpfs/scratchfs1/ham19006/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. | |
| 200228-14:00:34,443 nipype.interface INFO: | |
| stderr 2020-02-28T14:00:34.443797:++ Coarse del was 10, replaced with 6 | |
| 2020-02-28 14:00:34,443 nipype.interface:INFO stderr 2020-02-28T14:00:34.443797:++ Coarse del was 10, replaced with 6 | |
| 200228-14:00:38,21 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.funcMRIQC.ReportsWorkflow.SpikesFinderBgMask". | |
| 2020-02-28 14:00:38,021 nipype.workflow:INFO [Node] Finished "workflow_enumerator.funcMRIQC.ReportsWorkflow.SpikesFinderBgMask". | |
| 200228-14:00:38,875 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.AirMaskWorkflow.RotationMask" in "/gpfs/scratchfs1/ham19006/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 14:00:38,875 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.AirMaskWorkflow.RotationMask" in "/gpfs/scratchfs1/ham19006/hw3/work/workflow_enumerator/anatMRIQCT2w/AirMaskWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/RotationMask". | |
| 200228-14:00:38,877 nipype.workflow INFO: | |
| [Node] Running "RotationMask" ("mriqc.interfaces.anatomical.RotationMask") | |
| 2020-02-28 14:00:38,877 nipype.workflow:INFO [Node] Running "RotationMask" ("mriqc.interfaces.anatomical.RotationMask") | |
| 200228-14:00:40,873 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT2w.AirMaskWorkflow.RotationMask". | |
| 2020-02-28 14:00:40,873 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT2w.AirMaskWorkflow.RotationMask". | |
| 200228-14:00:42,875 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.AFNISkullStripWorkflow.inu_n4" in "/gpfs/scratchfs1/ham19006/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 14:00:42,875 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.AFNISkullStripWorkflow.inu_n4" in "/gpfs/scratchfs1/ham19006/hw3/work/workflow_enumerator/anatMRIQCT2w/AFNISkullStripWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/inu_n4". | |
| 200228-14:00:42,878 nipype.workflow INFO: | |
| [Node] Running "inu_n4" ("nipype.interfaces.ants.segmentation.N4BiasFieldCorrection"), a CommandLine Interface with command: | |
| N4BiasFieldCorrection -d 3 --input-image /gpfs/scratchfs1/ham19006/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 14:00:42,878 nipype.workflow:INFO [Node] Running "inu_n4" ("nipype.interfaces.ants.segmentation.N4BiasFieldCorrection"), a CommandLine Interface with command: | |
| N4BiasFieldCorrection -d 3 --input-image /gpfs/scratchfs1/ham19006/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 ] | |
| 200228-14:01:12,239 nipype.interface INFO: | |
| stderr 2020-02-28T14:01:12.239837:++ Max displacement in automask = 1.03 (mm) at sub-brick 16 | |
| 2020-02-28 14:01:12,239 nipype.interface:INFO stderr 2020-02-28T14:01:12.239837:++ Max displacement in automask = 1.03 (mm) at sub-brick 16 | |
| 200228-14:01:12,240 nipype.interface INFO: | |
| stderr 2020-02-28T14:01:12.240077:++ Max delta displ in automask = 0.79 (mm) at sub-brick 17 | |
| 2020-02-28 14:01:12,240 nipype.interface:INFO stderr 2020-02-28T14:01:12.240077:++ Max delta displ in automask = 0.79 (mm) at sub-brick 17 | |
| 200228-14:01:14,174 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.funcMRIQC.fMRI_HMC_afni.gen_ref". | |
| 2020-02-28 14:01:14,174 nipype.workflow:INFO [Node] Finished "workflow_enumerator.funcMRIQC.fMRI_HMC_afni.gen_ref". | |
| 200228-14:01:14,909 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.funcMRIQC.fMRI_HMC_afni.motion_correct" in "/gpfs/scratchfs1/ham19006/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 14:01:14,909 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.funcMRIQC.fMRI_HMC_afni.motion_correct" in "/gpfs/scratchfs1/ham19006/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". | |
| 200228-14:01:14,912 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/ham19006/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/ham19006/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 14:01:14,912 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/ham19006/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/ham19006/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 | |
| 200228-14:06:40,0 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT1w.AFNISkullStripWorkflow.inu_n4". | |
| 2020-02-28 14:06:40,000 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT1w.AFNISkullStripWorkflow.inu_n4". | |
| 200228-14:06:41,342 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.HeadMaskWorkflow.fsl_bet" in "/gpfs/scratchfs1/ham19006/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 14:06:41,342 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.HeadMaskWorkflow.fsl_bet" in "/gpfs/scratchfs1/ham19006/hw3/work/workflow_enumerator/anatMRIQCT1w/HeadMaskWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/fsl_bet". | |
| 200228-14:06:41,345 nipype.workflow INFO: | |
| [Node] Running "fsl_bet" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command: | |
| bet /gpfs/scratchfs1/ham19006/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/ham19006/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 14:06:41,345 nipype.workflow:INFO [Node] Running "fsl_bet" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command: | |
| bet /gpfs/scratchfs1/ham19006/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/ham19006/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 | |
| 200228-14:07:22,70 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT2w.AFNISkullStripWorkflow.inu_n4". | |
| 2020-02-28 14:07:22,070 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT2w.AFNISkullStripWorkflow.inu_n4". | |
| 200228-14:07:23,276 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.AFNISkullStripWorkflow.skullstrip" in "/gpfs/scratchfs1/ham19006/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 14:07:23,276 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.AFNISkullStripWorkflow.skullstrip" in "/gpfs/scratchfs1/ham19006/hw3/work/workflow_enumerator/anatMRIQCT1w/AFNISkullStripWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/skullstrip". | |
| 200228-14:07:23,279 nipype.workflow INFO: | |
| [Node] Running "skullstrip" ("nipype.interfaces.afni.preprocess.SkullStrip"), a CommandLine Interface with command: | |
| 3dSkullStrip -input /gpfs/scratchfs1/ham19006/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 14:07:23,279 nipype.workflow:INFO [Node] Running "skullstrip" ("nipype.interfaces.afni.preprocess.SkullStrip"), a CommandLine Interface with command: | |
| 3dSkullStrip -input /gpfs/scratchfs1/ham19006/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 | |
| 200228-14:08:31,716 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT1w.HeadMaskWorkflow.fsl_bet". | |
| 2020-02-28 14:08:31,716 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT1w.HeadMaskWorkflow.fsl_bet". | |
| 200228-14:08:33,340 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.HeadMaskWorkflow.fsl_bet" in "/gpfs/scratchfs1/ham19006/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 14:08:33,340 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.HeadMaskWorkflow.fsl_bet" in "/gpfs/scratchfs1/ham19006/hw3/work/workflow_enumerator/anatMRIQCT2w/HeadMaskWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/fsl_bet". | |
| 200228-14:08:33,343 nipype.workflow INFO: | |
| [Node] Running "fsl_bet" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command: | |
| bet /gpfs/scratchfs1/ham19006/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/ham19006/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 14:08:33,343 nipype.workflow:INFO [Node] Running "fsl_bet" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command: | |
| bet /gpfs/scratchfs1/ham19006/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/ham19006/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 | |
| 200228-14:08:43,818 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT1w.AFNISkullStripWorkflow.skullstrip". | |
| 2020-02-28 14:08:43,818 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT1w.AFNISkullStripWorkflow.skullstrip". | |
| 200228-14:08:45,354 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.AFNISkullStripWorkflow.sstrip_orig_vol" in "/gpfs/scratchfs1/ham19006/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 14:08:45,354 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.AFNISkullStripWorkflow.sstrip_orig_vol" in "/gpfs/scratchfs1/ham19006/hw3/work/workflow_enumerator/anatMRIQCT1w/AFNISkullStripWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/sstrip_orig_vol". | |
| 200228-14:08:45,357 nipype.workflow INFO: | |
| [Node] Running "sstrip_orig_vol" ("nipype.interfaces.afni.utils.Calc"), a CommandLine Interface with command: | |
| 3dcalc -a /gpfs/scratchfs1/ham19006/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/ham19006/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 14:08:45,357 nipype.workflow:INFO [Node] Running "sstrip_orig_vol" ("nipype.interfaces.afni.utils.Calc"), a CommandLine Interface with command: | |
| 3dcalc -a /gpfs/scratchfs1/ham19006/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/ham19006/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 | |
| 200228-14:08:48,177 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT1w.AFNISkullStripWorkflow.sstrip_orig_vol". | |
| 2020-02-28 14:08:48,177 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT1w.AFNISkullStripWorkflow.sstrip_orig_vol". | |
| 200228-14:08:49,364 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.segmentation" in "/gpfs/scratchfs1/ham19006/hw3/work/workflow_enumerator/anatMRIQCT1w/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/segmentation". | |
| 2020-02-28 14:08:49,364 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.segmentation" in "/gpfs/scratchfs1/ham19006/hw3/work/workflow_enumerator/anatMRIQCT1w/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/segmentation". | |
| 200228-14:08:49,372 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/ham19006/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 14:08:49,372 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/ham19006/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 | |
| 200228-14:10:27,549 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT2w.HeadMaskWorkflow.fsl_bet". | |
| 2020-02-28 14:10:27,549 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT2w.HeadMaskWorkflow.fsl_bet". | |
| 200228-14:10:29,471 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.AFNISkullStripWorkflow.binarize" in "/gpfs/scratchfs1/ham19006/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 14:10:29,471 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.AFNISkullStripWorkflow.binarize" in "/gpfs/scratchfs1/ham19006/hw3/work/workflow_enumerator/anatMRIQCT1w/AFNISkullStripWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/binarize". | |
| 200228-14:10:29,475 nipype.workflow INFO: | |
| [Node] Running "binarize" ("nipype.interfaces.fsl.maths.Threshold"), a CommandLine Interface with command: | |
| fslmaths /gpfs/scratchfs1/ham19006/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/ham19006/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 14:10:29,475 nipype.workflow:INFO [Node] Running "binarize" ("nipype.interfaces.fsl.maths.Threshold"), a CommandLine Interface with command: | |
| fslmaths /gpfs/scratchfs1/ham19006/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/ham19006/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 | |
| 200228-14:10:30,881 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT1w.AFNISkullStripWorkflow.binarize". | |
| 2020-02-28 14:10:30,881 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT1w.AFNISkullStripWorkflow.binarize". | |
| 200228-14:10:31,466 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.ReportsWorkflow.PlotMosaicZoomed" in "/gpfs/scratchfs1/ham19006/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 14:10:31,466 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.ReportsWorkflow.PlotMosaicZoomed" in "/gpfs/scratchfs1/ham19006/hw3/work/workflow_enumerator/anatMRIQCT1w/ReportsWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/PlotMosaicZoomed". | |
| 200228-14:10:31,468 nipype.workflow INFO: | |
| [Node] Running "PlotMosaicZoomed" ("mriqc.interfaces.viz.PlotMosaic") | |
| 2020-02-28 14:10:31,468 nipype.workflow:INFO [Node] Running "PlotMosaicZoomed" ("mriqc.interfaces.viz.PlotMosaic") | |
| 200228-14:10:43,491 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT1w.ReportsWorkflow.PlotMosaicZoomed". | |
| 2020-02-28 14:10:43,491 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT1w.ReportsWorkflow.PlotMosaicZoomed". | |
| 200228-14:10:45,481 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.ReportsWorkflow.MergePlots" in "/gpfs/scratchfs1/ham19006/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 14:10:45,481 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.ReportsWorkflow.MergePlots" in "/gpfs/scratchfs1/ham19006/hw3/work/workflow_enumerator/anatMRIQCT1w/ReportsWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/MergePlots". | |
| 200228-14:10:45,483 nipype.workflow INFO: | |
| [Node] Running "MergePlots" ("nipype.interfaces.utility.base.Merge") | |
| 2020-02-28 14:10:45,483 nipype.workflow:INFO [Node] Running "MergePlots" ("nipype.interfaces.utility.base.Merge") | |
| 200228-14:10:45,486 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT1w.ReportsWorkflow.MergePlots". | |
| 2020-02-28 14:10:45,486 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT1w.ReportsWorkflow.MergePlots". | |
| 200228-14:10:47,663 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.ComputeIQMs.smoothness" in "/gpfs/scratchfs1/ham19006/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 14:10:47,663 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.ComputeIQMs.smoothness" in "/gpfs/scratchfs1/ham19006/hw3/work/workflow_enumerator/anatMRIQCT1w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/smoothness". | |
| 200228-14:10:47,666 nipype.workflow INFO: | |
| [Node] Running "smoothness" ("nipype.interfaces.afni.utils.FWHMx"), a CommandLine Interface with command: | |
| 3dFWHMx -ShowMeClassicFWHM -combine -detrend -input /gpfs/scratchfs1/ham19006/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/ham19006/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 14:10:47,666 nipype.workflow:INFO [Node] Running "smoothness" ("nipype.interfaces.afni.utils.FWHMx"), a CommandLine Interface with command: | |
| 3dFWHMx -ShowMeClassicFWHM -combine -detrend -input /gpfs/scratchfs1/ham19006/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/ham19006/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 | |
| 200228-14:10:59,217 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT1w.ComputeIQMs.smoothness". | |
| 2020-02-28 14:10:59,217 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT1w.ComputeIQMs.smoothness". | |
| 200228-14:11:00,356 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.SpatialNormalization.SpatialNormalization" in "/gpfs/scratchfs1/ham19006/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 14:11:00,356 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.SpatialNormalization.SpatialNormalization" in "/gpfs/scratchfs1/ham19006/hw3/work/workflow_enumerator/anatMRIQCT1w/SpatialNormalization/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/SpatialNormalization". | |
| 200228-14:11:00,390 nipype.workflow INFO: | |
| [Node] Running "SpatialNormalization" ("niworkflows.interfaces.registration.RobustMNINormalizationRPT") | |
| 2020-02-28 14:11:00,390 nipype.workflow:INFO [Node] Running "SpatialNormalization" ("niworkflows.interfaces.registration.RobustMNINormalizationRPT") | |
| 2020-02-28 14:11:02,355 niworkflows:INFO Estimating initial transform using AffineInitializer | |
| 2020-02-28 14:13:23,703 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 14:13:23,707 niworkflows:INFO Retry #1, commandline: | |
| antsRegistration --collapse-output-transforms 1 --dimensionality 3 --float 0 --initial-moving-transform [ /gpfs/scratchfs1/ham19006/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/ham19006/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/ham19006/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/ham19006/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/ham19006/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/ham19006/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/ham19006/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 | |
| 200228-14:16:58,472 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT1w.segmentation". | |
| 2020-02-28 14:16:58,472 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT1w.segmentation". | |
| 200228-14:16:59,618 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.ComputeIQMs.harmonize" in "/gpfs/scratchfs1/ham19006/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 14:16:59,618 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.ComputeIQMs.harmonize" in "/gpfs/scratchfs1/ham19006/hw3/work/workflow_enumerator/anatMRIQCT1w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/harmonize". | |
| 200228-14:16:59,634 nipype.workflow INFO: | |
| [Node] Running "harmonize" ("mriqc.interfaces.anatomical.Harmonize") | |
| 2020-02-28 14:16:59,634 nipype.workflow:INFO [Node] Running "harmonize" ("mriqc.interfaces.anatomical.Harmonize") | |
| 200228-14:17:04,962 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT1w.ComputeIQMs.harmonize". | |
| 2020-02-28 14:17:04,962 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT1w.ComputeIQMs.harmonize". | |
| 200228-14:17:05,542 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.AFNISkullStripWorkflow.skullstrip" in "/gpfs/scratchfs1/ham19006/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 14:17:05,542 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.AFNISkullStripWorkflow.skullstrip" in "/gpfs/scratchfs1/ham19006/hw3/work/workflow_enumerator/anatMRIQCT2w/AFNISkullStripWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/skullstrip". | |
| 200228-14:17:05,545 nipype.workflow INFO: | |
| [Node] Running "skullstrip" ("nipype.interfaces.afni.preprocess.SkullStrip"), a CommandLine Interface with command: | |
| 3dSkullStrip -input /gpfs/scratchfs1/ham19006/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 14:17:05,545 nipype.workflow:INFO [Node] Running "skullstrip" ("nipype.interfaces.afni.preprocess.SkullStrip"), a CommandLine Interface with command: | |
| 3dSkullStrip -input /gpfs/scratchfs1/ham19006/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 14:17:13,288 niworkflows:INFO Successful spatial normalization (retry #1). | |
| 2020-02-28 14:17:16,684 niworkflows:INFO Report - setting fixed (/gpfs/scratchfs1/ham19006/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/ham19006/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 14:17:16,685 niworkflows:INFO Generating visual report | |
| 200228-14:17:24,550 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT1w.SpatialNormalization.SpatialNormalization". | |
| 2020-02-28 14:17:24,550 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT1w.SpatialNormalization.SpatialNormalization". | |
| 200228-14:17:25,563 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.AirMaskWorkflow.invert_xfm" in "/gpfs/scratchfs1/ham19006/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 14:17:25,563 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.AirMaskWorkflow.invert_xfm" in "/gpfs/scratchfs1/ham19006/hw3/work/workflow_enumerator/anatMRIQCT1w/AirMaskWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/invert_xfm". | |
| 200228-14:17:25,567 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/ham19006/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/ham19006/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 14:17:25,567 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/ham19006/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/ham19006/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 | |
| 200228-14:18:32,575 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT2w.AFNISkullStripWorkflow.skullstrip". | |
| 2020-02-28 14:18:32,575 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT2w.AFNISkullStripWorkflow.skullstrip". | |
| 200228-14:18:33,622 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.AFNISkullStripWorkflow.sstrip_orig_vol" in "/gpfs/scratchfs1/ham19006/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 14:18:33,622 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.AFNISkullStripWorkflow.sstrip_orig_vol" in "/gpfs/scratchfs1/ham19006/hw3/work/workflow_enumerator/anatMRIQCT2w/AFNISkullStripWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/sstrip_orig_vol". | |
| 200228-14:18:33,624 nipype.workflow INFO: | |
| [Node] Running "sstrip_orig_vol" ("nipype.interfaces.afni.utils.Calc"), a CommandLine Interface with command: | |
| 3dcalc -a /gpfs/scratchfs1/ham19006/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/ham19006/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 14:18:33,624 nipype.workflow:INFO [Node] Running "sstrip_orig_vol" ("nipype.interfaces.afni.utils.Calc"), a CommandLine Interface with command: | |
| 3dcalc -a /gpfs/scratchfs1/ham19006/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/ham19006/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 | |
| 200228-14:18:35,596 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT2w.AFNISkullStripWorkflow.sstrip_orig_vol". | |
| 2020-02-28 14:18:35,596 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT2w.AFNISkullStripWorkflow.sstrip_orig_vol". | |
| 200228-14:18:37,623 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.segmentation" in "/gpfs/scratchfs1/ham19006/hw3/work/workflow_enumerator/anatMRIQCT2w/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/segmentation". | |
| 2020-02-28 14:18:37,623 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.segmentation" in "/gpfs/scratchfs1/ham19006/hw3/work/workflow_enumerator/anatMRIQCT2w/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/segmentation". | |
| 200228-14:18:37,627 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/ham19006/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 14:18:37,627 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/ham19006/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 | |
| 200228-14:18:40,359 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.funcMRIQC.fMRI_HMC_afni.motion_correct". | |
| 2020-02-28 14:18:40,359 nipype.workflow:INFO [Node] Finished "workflow_enumerator.funcMRIQC.fMRI_HMC_afni.motion_correct". | |
| 200228-14:18:41,634 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.funcMRIQC.ComputeIQMs.quality" in "/gpfs/scratchfs1/ham19006/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 14:18:41,634 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.funcMRIQC.ComputeIQMs.quality" in "/gpfs/scratchfs1/ham19006/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". | |
| 200228-14:18:41,638 nipype.workflow INFO: | |
| [Node] Running "quality" ("nipype.interfaces.afni.preprocess.QualityIndex"), a CommandLine Interface with command: | |
| 3dTqual -automask /gpfs/scratchfs1/ham19006/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 14:18:41,638 nipype.workflow:INFO [Node] Running "quality" ("nipype.interfaces.afni.preprocess.QualityIndex"), a CommandLine Interface with command: | |
| 3dTqual -automask /gpfs/scratchfs1/ham19006/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 | |
| 200228-14:18:55,310 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.funcMRIQC.ComputeIQMs.quality". | |
| 2020-02-28 14:18:55,310 nipype.workflow:INFO [Node] Finished "workflow_enumerator.funcMRIQC.ComputeIQMs.quality". | |
| 200228-14:18:55,990 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.funcMRIQC.compute_tsnr" in "/gpfs/scratchfs1/ham19006/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 14:18:55,990 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.funcMRIQC.compute_tsnr" in "/gpfs/scratchfs1/ham19006/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". | |
| 200228-14:18:55,995 nipype.workflow INFO: | |
| [Node] Running "compute_tsnr" ("nipype.algorithms.confounds.TSNR") | |
| 2020-02-28 14:18:55,995 nipype.workflow:INFO [Node] Running "compute_tsnr" ("nipype.algorithms.confounds.TSNR") | |
| 200228-14:19:07,319 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.funcMRIQC.compute_tsnr". | |
| 2020-02-28 14:19:07,319 nipype.workflow:INFO [Node] Finished "workflow_enumerator.funcMRIQC.compute_tsnr". | |
| 200228-14:19:07,731 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.funcMRIQC.ReportsWorkflow.PlotMosaicSD" in "/gpfs/scratchfs1/ham19006/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 14:19:07,731 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.funcMRIQC.ReportsWorkflow.PlotMosaicSD" in "/gpfs/scratchfs1/ham19006/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". | |
| 200228-14:19:07,734 nipype.workflow INFO: | |
| [Node] Running "PlotMosaicSD" ("mriqc.interfaces.viz.PlotMosaic") | |
| 2020-02-28 14:19:07,734 nipype.workflow:INFO [Node] Running "PlotMosaicSD" ("mriqc.interfaces.viz.PlotMosaic") | |
| 200228-14:19:17,161 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.funcMRIQC.ReportsWorkflow.PlotMosaicSD". | |
| 2020-02-28 14:19:17,161 nipype.workflow:INFO [Node] Finished "workflow_enumerator.funcMRIQC.ReportsWorkflow.PlotMosaicSD". | |
| 200228-14:19:17,671 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.funcMRIQC.mean" in "/gpfs/scratchfs1/ham19006/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 14:19:17,671 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.funcMRIQC.mean" in "/gpfs/scratchfs1/ham19006/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". | |
| 200228-14:19:17,675 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/ham19006/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 14:19:17,675 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/ham19006/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 | |
| 200228-14:19:23,400 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.funcMRIQC.mean". | |
| 2020-02-28 14:19:23,400 nipype.workflow:INFO [Node] Finished "workflow_enumerator.funcMRIQC.mean". | |
| 200228-14:19:23,670 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.funcMRIQC.ReportsWorkflow.PlotMosaicMean" in "/gpfs/scratchfs1/ham19006/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 14:19:23,670 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.funcMRIQC.ReportsWorkflow.PlotMosaicMean" in "/gpfs/scratchfs1/ham19006/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". | |
| 200228-14:19:23,696 nipype.workflow INFO: | |
| [Node] Running "PlotMosaicMean" ("mriqc.interfaces.viz.PlotMosaic") | |
| 2020-02-28 14:19:23,696 nipype.workflow:INFO [Node] Running "PlotMosaicMean" ("mriqc.interfaces.viz.PlotMosaic") | |
| 200228-14:19:32,457 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.funcMRIQC.ReportsWorkflow.PlotMosaicMean". | |
| 2020-02-28 14:19:32,457 nipype.workflow:INFO [Node] Finished "workflow_enumerator.funcMRIQC.ReportsWorkflow.PlotMosaicMean". | |
| 200228-14:19:33,678 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.funcMRIQC.SpatialNormalization.SharpenEPI" in "/gpfs/scratchfs1/ham19006/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 14:19:33,678 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.funcMRIQC.SpatialNormalization.SharpenEPI" in "/gpfs/scratchfs1/ham19006/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". | |
| 200228-14:19:33,711 nipype.workflow INFO: | |
| [Node] Running "SharpenEPI" ("nipype.interfaces.ants.segmentation.N4BiasFieldCorrection"), a CommandLine Interface with command: | |
| N4BiasFieldCorrection -d 3 --input-image /gpfs/scratchfs1/ham19006/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 14:19:33,711 nipype.workflow:INFO [Node] Running "SharpenEPI" ("nipype.interfaces.ants.segmentation.N4BiasFieldCorrection"), a CommandLine Interface with command: | |
| N4BiasFieldCorrection -d 3 --input-image /gpfs/scratchfs1/ham19006/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 | |
| 200228-14:19:44,143 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.funcMRIQC.SpatialNormalization.SharpenEPI". | |
| 2020-02-28 14:19:44,143 nipype.workflow:INFO [Node] Finished "workflow_enumerator.funcMRIQC.SpatialNormalization.SharpenEPI". | |
| 200228-14:19:45,696 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.funcMRIQC.fMRIBrainMask.bet_msk" in "/gpfs/scratchfs1/ham19006/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 14:19:45,696 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.funcMRIQC.fMRIBrainMask.bet_msk" in "/gpfs/scratchfs1/ham19006/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". | |
| 200228-14:19:45,707 nipype.workflow INFO: | |
| [Node] Running "bet_msk" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command: | |
| bet /gpfs/scratchfs1/ham19006/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/ham19006/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 14:19:45,707 nipype.workflow:INFO [Node] Running "bet_msk" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command: | |
| bet /gpfs/scratchfs1/ham19006/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/ham19006/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 | |
| 200228-14:19:48,361 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.funcMRIQC.fMRIBrainMask.bet_msk". | |
| 2020-02-28 14:19:48,361 nipype.workflow:INFO [Node] Finished "workflow_enumerator.funcMRIQC.fMRIBrainMask.bet_msk". | |
| 200228-14:19:49,696 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.funcMRIQC.fMRIBrainMask.erode" in "/gpfs/scratchfs1/ham19006/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 14:19:49,696 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.funcMRIQC.fMRIBrainMask.erode" in "/gpfs/scratchfs1/ham19006/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". | |
| 200228-14:19:49,698 nipype.workflow INFO: | |
| [Node] Running "erode" ("nipype.interfaces.fsl.maths.ErodeImage"), a CommandLine Interface with command: | |
| fslmaths /gpfs/scratchfs1/ham19006/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/ham19006/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 14:19:49,698 nipype.workflow:INFO [Node] Running "erode" ("nipype.interfaces.fsl.maths.ErodeImage"), a CommandLine Interface with command: | |
| fslmaths /gpfs/scratchfs1/ham19006/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/ham19006/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 | |
| 200228-14:19:50,703 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.funcMRIQC.fMRIBrainMask.erode". | |
| 2020-02-28 14:19:50,703 nipype.workflow:INFO [Node] Finished "workflow_enumerator.funcMRIQC.fMRIBrainMask.erode". | |
| 200228-14:19:51,702 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.funcMRIQC.ComputeIQMs.gcor" in "/gpfs/scratchfs1/ham19006/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 14:19:51,702 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.funcMRIQC.ComputeIQMs.gcor" in "/gpfs/scratchfs1/ham19006/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". | |
| 200228-14:19:51,705 nipype.workflow INFO: | |
| [Node] Running "gcor" ("mriqc.interfaces.transitional.GCOR"), a CommandLine Interface with command: | |
| @compute_gcor -mask /gpfs/scratchfs1/ham19006/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/ham19006/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 14:19:51,705 nipype.workflow:INFO [Node] Running "gcor" ("mriqc.interfaces.transitional.GCOR"), a CommandLine Interface with command: | |
| @compute_gcor -mask /gpfs/scratchfs1/ham19006/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/ham19006/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 | |
| 200228-14:20:07,551 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.funcMRIQC.ComputeIQMs.gcor". | |
| 2020-02-28 14:20:07,551 nipype.workflow:INFO [Node] Finished "workflow_enumerator.funcMRIQC.ComputeIQMs.gcor". | |
| 200228-14:20:07,717 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.funcMRIQC.ComputeIQMs.outliers" in "/gpfs/scratchfs1/ham19006/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 14:20:07,717 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.funcMRIQC.ComputeIQMs.outliers" in "/gpfs/scratchfs1/ham19006/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". | |
| 200228-14:20:07,746 nipype.workflow INFO: | |
| [Node] Running "outliers" ("nipype.interfaces.afni.preprocess.OutlierCount"), a CommandLine Interface with command: | |
| 3dToutcount -fraction -mask /gpfs/scratchfs1/ham19006/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/ham19006/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 14:20:07,746 nipype.workflow:INFO [Node] Running "outliers" ("nipype.interfaces.afni.preprocess.OutlierCount"), a CommandLine Interface with command: | |
| 3dToutcount -fraction -mask /gpfs/scratchfs1/ham19006/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/ham19006/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 | |
| 200228-14:20:14,930 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.funcMRIQC.ComputeIQMs.outliers". | |
| 2020-02-28 14:20:14,930 nipype.workflow:INFO [Node] Finished "workflow_enumerator.funcMRIQC.ComputeIQMs.outliers". | |
| 200228-14:20:15,724 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.funcMRIQC.ComputeIQMs.smoothness" in "/gpfs/scratchfs1/ham19006/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 14:20:15,724 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.funcMRIQC.ComputeIQMs.smoothness" in "/gpfs/scratchfs1/ham19006/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". | |
| 200228-14:20:15,741 nipype.workflow INFO: | |
| [Node] Running "smoothness" ("nipype.interfaces.afni.utils.FWHMx"), a CommandLine Interface with command: | |
| 3dFWHMx -ShowMeClassicFWHM -combine -detrend -input /gpfs/scratchfs1/ham19006/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/ham19006/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 14:20:15,741 nipype.workflow:INFO [Node] Running "smoothness" ("nipype.interfaces.afni.utils.FWHMx"), a CommandLine Interface with command: | |
| 3dFWHMx -ShowMeClassicFWHM -combine -detrend -input /gpfs/scratchfs1/ham19006/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/ham19006/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 | |
| 200228-14:20:16,840 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.funcMRIQC.ComputeIQMs.smoothness". | |
| 2020-02-28 14:20:16,840 nipype.workflow:INFO [Node] Finished "workflow_enumerator.funcMRIQC.ComputeIQMs.smoothness". | |
| 200228-14:20:17,723 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.funcMRIQC.ComputeIQMs.ComputeDVARS" in "/gpfs/scratchfs1/ham19006/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 14:20:17,723 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.funcMRIQC.ComputeIQMs.ComputeDVARS" in "/gpfs/scratchfs1/ham19006/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". | |
| 200228-14:20:17,725 nipype.workflow INFO: | |
| [Node] Running "ComputeDVARS" ("nipype.algorithms.confounds.ComputeDVARS") | |
| 2020-02-28 14:20:17,725 nipype.workflow:INFO [Node] Running "ComputeDVARS" ("nipype.algorithms.confounds.ComputeDVARS") | |
| 200228-14:21:03,39 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.funcMRIQC.ComputeIQMs.ComputeDVARS". | |
| 2020-02-28 14:21:03,039 nipype.workflow:INFO [Node] Finished "workflow_enumerator.funcMRIQC.ComputeIQMs.ComputeDVARS". | |
| 200228-14:21:04,58 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.funcMRIQC.SpatialNormalization.EPI2MNI" in "/gpfs/scratchfs1/ham19006/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 14:21:04,058 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.funcMRIQC.SpatialNormalization.EPI2MNI" in "/gpfs/scratchfs1/ham19006/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". | |
| 200228-14:21:04,65 nipype.workflow INFO: | |
| [Node] Running "EPI2MNI" ("niworkflows.interfaces.registration.RobustMNINormalizationRPT") | |
| 2020-02-28 14:21:04,065 nipype.workflow:INFO [Node] Running "EPI2MNI" ("niworkflows.interfaces.registration.RobustMNINormalizationRPT") | |
| 2020-02-28 14:21:04,083 niworkflows:INFO Estimating initial transform using AffineInitializer | |
| 200228-14:21:58,76 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT1w.AirMaskWorkflow.invert_xfm". | |
| 2020-02-28 14:21:58,076 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT1w.AirMaskWorkflow.invert_xfm". | |
| 200228-14:21:59,832 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.funcMRIQC.fMRI_HMC_afni.ComputeFD" in "/gpfs/scratchfs1/ham19006/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 14:21:59,832 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.funcMRIQC.fMRI_HMC_afni.ComputeFD" in "/gpfs/scratchfs1/ham19006/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". | |
| 200228-14:21:59,835 nipype.workflow INFO: | |
| [Node] Running "ComputeFD" ("nipype.algorithms.confounds.FramewiseDisplacement") | |
| 2020-02-28 14:21:59,835 nipype.workflow:INFO [Node] Running "ComputeFD" ("nipype.algorithms.confounds.FramewiseDisplacement") | |
| 200228-14:21:59,878 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.funcMRIQC.fMRI_HMC_afni.ComputeFD". | |
| 2020-02-28 14:21:59,878 nipype.workflow:INFO [Node] Finished "workflow_enumerator.funcMRIQC.fMRI_HMC_afni.ComputeFD". | |
| 200228-14:22:01,836 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.funcMRIQC.ComputeIQMs.measures" in "/gpfs/scratchfs1/ham19006/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 14:22:01,836 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.funcMRIQC.ComputeIQMs.measures" in "/gpfs/scratchfs1/ham19006/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". | |
| 200228-14:22:01,839 nipype.workflow INFO: | |
| [Node] Running "measures" ("mriqc.interfaces.functional.FunctionalQC") | |
| 2020-02-28 14:22:01,839 nipype.workflow:INFO [Node] Running "measures" ("mriqc.interfaces.functional.FunctionalQC") | |
| 200228-14:22:07,235 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.funcMRIQC.ComputeIQMs.measures". | |
| 2020-02-28 14:22:07,235 nipype.workflow:INFO [Node] Finished "workflow_enumerator.funcMRIQC.ComputeIQMs.measures". | |
| 200228-14:22:08,21 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.AirMaskWorkflow.ArtifactMask" in "/gpfs/scratchfs1/ham19006/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 14:22:08,021 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.AirMaskWorkflow.ArtifactMask" in "/gpfs/scratchfs1/ham19006/hw3/work/workflow_enumerator/anatMRIQCT1w/AirMaskWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/ArtifactMask". | |
| 200228-14:22:08,24 nipype.workflow INFO: | |
| [Node] Running "ArtifactMask" ("mriqc.interfaces.anatomical.ArtifactMask") | |
| 2020-02-28 14:22:08,024 nipype.workflow:INFO [Node] Running "ArtifactMask" ("mriqc.interfaces.anatomical.ArtifactMask") | |
| 200228-14:22:15,3 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT1w.AirMaskWorkflow.ArtifactMask". | |
| 2020-02-28 14:22:15,003 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT1w.AirMaskWorkflow.ArtifactMask". | |
| 200228-14:22:15,843 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.funcMRIQC.UploadMetrics" in "/gpfs/scratchfs1/ham19006/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 14:22:15,843 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.funcMRIQC.UploadMetrics" in "/gpfs/scratchfs1/ham19006/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". | |
| 200228-14:22:15,882 nipype.workflow INFO: | |
| [Node] Running "UploadMetrics" ("mriqc.interfaces.webapi.UploadIQMs") | |
| 2020-02-28 14:22:15,882 nipype.workflow:INFO [Node] Running "UploadMetrics" ("mriqc.interfaces.webapi.UploadIQMs") | |
| 200228-14:22:17,131 nipype.interface INFO: | |
| MRIQC Web API: submitting to <https://mriqc.nimh.nih.gov:443/api/v1/bold> | |
| 2020-02-28 14:22:17,131 nipype.interface:INFO MRIQC Web API: submitting to <https://mriqc.nimh.nih.gov:443/api/v1/bold> | |
| 200228-14:22:17,366 nipype.interface INFO: | |
| QC metrics successfully uploaded. | |
| 2020-02-28 14:22:17,366 nipype.interface:INFO QC metrics successfully uploaded. | |
| 200228-14:22:17,370 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.funcMRIQC.UploadMetrics". | |
| 2020-02-28 14:22:17,370 nipype.workflow:INFO [Node] Finished "workflow_enumerator.funcMRIQC.UploadMetrics". | |
| 200228-14:22:17,845 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.ComputeIQMs.ComputeQI2" in "/gpfs/scratchfs1/ham19006/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 14:22:17,845 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.ComputeIQMs.ComputeQI2" in "/gpfs/scratchfs1/ham19006/hw3/work/workflow_enumerator/anatMRIQCT1w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/ComputeQI2". | |
| 200228-14:22:17,848 nipype.workflow INFO: | |
| [Node] Running "ComputeQI2" ("mriqc.interfaces.anatomical.ComputeQI2") | |
| 2020-02-28 14:22:17,848 nipype.workflow:INFO [Node] Running "ComputeQI2" ("mriqc.interfaces.anatomical.ComputeQI2") | |
| 2020-02-28 14:22:21,427 niworkflows:INFO Terminal outputs of initialization saved (/gpfs/scratchfs1/ham19006/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 14:22:21,427 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 14:22:21,430 niworkflows:INFO Retry #1, commandline: | |
| antsRegistration --collapse-output-transforms 1 --dimensionality 3 --float 0 --initial-moving-transform [ /gpfs/scratchfs1/ham19006/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/ham19006/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/ham19006/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/ham19006/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/ham19006/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/ham19006/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/ham19006/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 | |
| 200228-14:22:54,311 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT1w.ComputeIQMs.ComputeQI2". | |
| 2020-02-28 14:22:54,311 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT1w.ComputeIQMs.ComputeQI2". | |
| 200228-14:22:55,882 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.ComputeIQMs.provenance" in "/gpfs/scratchfs1/ham19006/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 14:22:55,882 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.ComputeIQMs.provenance" in "/gpfs/scratchfs1/ham19006/hw3/work/workflow_enumerator/anatMRIQCT1w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/provenance". | |
| 200228-14:22:55,884 nipype.workflow INFO: | |
| [Node] Running "provenance" ("nipype.interfaces.utility.wrappers.Function") | |
| 2020-02-28 14:22:55,884 nipype.workflow:INFO [Node] Running "provenance" ("nipype.interfaces.utility.wrappers.Function") | |
| 200228-14:22:56,193 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT1w.ComputeIQMs.provenance". | |
| 2020-02-28 14:22:56,193 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT1w.ComputeIQMs.provenance". | |
| 200228-14:22:57,886 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.AFNISkullStripWorkflow.binarize" in "/gpfs/scratchfs1/ham19006/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 14:22:57,886 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.AFNISkullStripWorkflow.binarize" in "/gpfs/scratchfs1/ham19006/hw3/work/workflow_enumerator/anatMRIQCT2w/AFNISkullStripWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/binarize". | |
| 200228-14:22:57,893 nipype.workflow INFO: | |
| [Node] Running "binarize" ("nipype.interfaces.fsl.maths.Threshold"), a CommandLine Interface with command: | |
| fslmaths /gpfs/scratchfs1/ham19006/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/ham19006/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 14:22:57,893 nipype.workflow:INFO [Node] Running "binarize" ("nipype.interfaces.fsl.maths.Threshold"), a CommandLine Interface with command: | |
| fslmaths /gpfs/scratchfs1/ham19006/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/ham19006/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 | |
| 200228-14:22:59,404 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT2w.AFNISkullStripWorkflow.binarize". | |
| 2020-02-28 14:22:59,404 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT2w.AFNISkullStripWorkflow.binarize". | |
| 200228-14:22:59,890 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.ReportsWorkflow.PlotMosaicZoomed" in "/gpfs/scratchfs1/ham19006/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 14:22:59,890 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.ReportsWorkflow.PlotMosaicZoomed" in "/gpfs/scratchfs1/ham19006/hw3/work/workflow_enumerator/anatMRIQCT2w/ReportsWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/PlotMosaicZoomed". | |
| 200228-14:22:59,893 nipype.workflow INFO: | |
| [Node] Running "PlotMosaicZoomed" ("mriqc.interfaces.viz.PlotMosaic") | |
| 2020-02-28 14:22:59,893 nipype.workflow:INFO [Node] Running "PlotMosaicZoomed" ("mriqc.interfaces.viz.PlotMosaic") | |
| 200228-14:23:11,878 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT2w.ReportsWorkflow.PlotMosaicZoomed". | |
| 2020-02-28 14:23:11,878 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT2w.ReportsWorkflow.PlotMosaicZoomed". | |
| 200228-14:23:13,905 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.ReportsWorkflow.MergePlots" in "/gpfs/scratchfs1/ham19006/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 14:23:13,905 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.ReportsWorkflow.MergePlots" in "/gpfs/scratchfs1/ham19006/hw3/work/workflow_enumerator/anatMRIQCT2w/ReportsWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/MergePlots". | |
| 200228-14:23:13,907 nipype.workflow INFO: | |
| [Node] Running "MergePlots" ("nipype.interfaces.utility.base.Merge") | |
| 2020-02-28 14:23:13,907 nipype.workflow:INFO [Node] Running "MergePlots" ("nipype.interfaces.utility.base.Merge") | |
| 200228-14:23:13,913 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT2w.ReportsWorkflow.MergePlots". | |
| 2020-02-28 14:23:13,913 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT2w.ReportsWorkflow.MergePlots". | |
| 200228-14:23:15,906 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.ComputeIQMs.smoothness" in "/gpfs/scratchfs1/ham19006/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 14:23:15,906 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.ComputeIQMs.smoothness" in "/gpfs/scratchfs1/ham19006/hw3/work/workflow_enumerator/anatMRIQCT2w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/smoothness". | |
| 200228-14:23:15,908 nipype.workflow INFO: | |
| [Node] Running "smoothness" ("nipype.interfaces.afni.utils.FWHMx"), a CommandLine Interface with command: | |
| 3dFWHMx -ShowMeClassicFWHM -combine -detrend -input /gpfs/scratchfs1/ham19006/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/ham19006/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 14:23:15,908 nipype.workflow:INFO [Node] Running "smoothness" ("nipype.interfaces.afni.utils.FWHMx"), a CommandLine Interface with command: | |
| 3dFWHMx -ShowMeClassicFWHM -combine -detrend -input /gpfs/scratchfs1/ham19006/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/ham19006/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 | |
| 200228-14:23:26,481 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT2w.ComputeIQMs.smoothness". | |
| 2020-02-28 14:23:26,481 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT2w.ComputeIQMs.smoothness". | |
| 200228-14:23:27,917 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.SpatialNormalization.SpatialNormalization" in "/gpfs/scratchfs1/ham19006/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 14:23:27,917 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.SpatialNormalization.SpatialNormalization" in "/gpfs/scratchfs1/ham19006/hw3/work/workflow_enumerator/anatMRIQCT2w/SpatialNormalization/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/SpatialNormalization". | |
| 200228-14:23:27,932 nipype.workflow INFO: | |
| [Node] Running "SpatialNormalization" ("niworkflows.interfaces.registration.RobustMNINormalizationRPT") | |
| 2020-02-28 14:23:27,932 nipype.workflow:INFO [Node] Running "SpatialNormalization" ("niworkflows.interfaces.registration.RobustMNINormalizationRPT") | |
| 2020-02-28 14:23:29,788 niworkflows:INFO Estimating initial transform using AffineInitializer | |
| 2020-02-28 14:24:13,159 niworkflows:INFO Successful spatial normalization (retry #1). | |
| 2020-02-28 14:24:13,159 niworkflows:INFO Report - setting fixed (/opt/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz) and moving (/gpfs/scratchfs1/ham19006/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 14:24:13,159 niworkflows:INFO Generating visual report | |
| 200228-14:24:23,925 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.funcMRIQC.SpatialNormalization.EPI2MNI". | |
| 2020-02-28 14:24:23,925 nipype.workflow:INFO [Node] Finished "workflow_enumerator.funcMRIQC.SpatialNormalization.EPI2MNI". | |
| 200228-14:24:25,974 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.funcMRIQC.SpatialNormalization.ResampleSegmentation" in "/gpfs/scratchfs1/ham19006/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 14:24:25,974 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.funcMRIQC.SpatialNormalization.ResampleSegmentation" in "/gpfs/scratchfs1/ham19006/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". | |
| 200228-14:24:25,977 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/ham19006/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/ham19006/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 14:24:25,977 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/ham19006/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/ham19006/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 | |
| 200228-14:24:31,687 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.funcMRIQC.SpatialNormalization.ResampleSegmentation". | |
| 2020-02-28 14:24:31,687 nipype.workflow:INFO [Node] Finished "workflow_enumerator.funcMRIQC.SpatialNormalization.ResampleSegmentation". | |
| 200228-14:24:31,983 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.funcMRIQC.ReportsWorkflow.BigPlot" in "/gpfs/scratchfs1/ham19006/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 14:24:31,983 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.funcMRIQC.ReportsWorkflow.BigPlot" in "/gpfs/scratchfs1/ham19006/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". | |
| 200228-14:24:31,986 nipype.workflow INFO: | |
| [Node] Running "BigPlot" ("niworkflows.interfaces.plotting.FMRISummary") | |
| 2020-02-28 14:24:31,986 nipype.workflow:INFO [Node] Running "BigPlot" ("niworkflows.interfaces.plotting.FMRISummary") | |
| 200228-14:24:52,53 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.funcMRIQC.ReportsWorkflow.BigPlot". | |
| 2020-02-28 14:24:52,053 nipype.workflow:INFO [Node] Finished "workflow_enumerator.funcMRIQC.ReportsWorkflow.BigPlot". | |
| 200228-14:24:52,666 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.funcMRIQC.ReportsWorkflow.MergePlots" in "/gpfs/scratchfs1/ham19006/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 14:24:52,666 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.funcMRIQC.ReportsWorkflow.MergePlots" in "/gpfs/scratchfs1/ham19006/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". | |
| 200228-14:24:52,696 nipype.workflow INFO: | |
| [Node] Running "MergePlots" ("nipype.interfaces.utility.base.Merge") | |
| 2020-02-28 14:24:52,696 nipype.workflow:INFO [Node] Running "MergePlots" ("nipype.interfaces.utility.base.Merge") | |
| 200228-14:24:52,700 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.funcMRIQC.ReportsWorkflow.MergePlots". | |
| 2020-02-28 14:24:52,700 nipype.workflow:INFO [Node] Finished "workflow_enumerator.funcMRIQC.ReportsWorkflow.MergePlots". | |
| 200228-14:24:54,160 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.funcMRIQC.ReportsWorkflow.GenerateReport" in "/gpfs/scratchfs1/ham19006/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 14:24:54,160 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.funcMRIQC.ReportsWorkflow.GenerateReport" in "/gpfs/scratchfs1/ham19006/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". | |
| 200228-14:24:54,173 nipype.workflow INFO: | |
| [Node] Running "GenerateReport" ("nipype.interfaces.utility.wrappers.Function") | |
| 2020-02-28 14:24:54,173 nipype.workflow:INFO [Node] Running "GenerateReport" ("nipype.interfaces.utility.wrappers.Function") | |
| 2020-02-28 14:24:54,346 mriqc.report:WARNING Building bold report: no exclude index was found | |
| 200228-14:24:54,491 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.funcMRIQC.ReportsWorkflow.GenerateReport". | |
| 2020-02-28 14:24:54,491 nipype.workflow:INFO [Node] Finished "workflow_enumerator.funcMRIQC.ReportsWorkflow.GenerateReport". | |
| 200228-14:24:56,313 nipype.workflow INFO: | |
| [Node] Setting-up "_MNItpms2t10" in "/gpfs/scratchfs1/ham19006/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 14:24:56,313 nipype.workflow:INFO [Node] Setting-up "_MNItpms2t10" in "/gpfs/scratchfs1/ham19006/hw3/work/workflow_enumerator/anatMRIQCT1w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/MNItpms2t1/mapflow/_MNItpms2t10". | |
| 200228-14:24:56,316 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/ham19006/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/ham19006/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 14:24:56,316 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/ham19006/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/ham19006/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 | |
| 200228-14:25:02,185 nipype.workflow INFO: | |
| [Node] Finished "_MNItpms2t10". | |
| 2020-02-28 14:25:02,185 nipype.workflow:INFO [Node] Finished "_MNItpms2t10". | |
| 200228-14:25:04,165 nipype.workflow INFO: | |
| [Node] Setting-up "_MNItpms2t11" in "/gpfs/scratchfs1/ham19006/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 14:25:04,165 nipype.workflow:INFO [Node] Setting-up "_MNItpms2t11" in "/gpfs/scratchfs1/ham19006/hw3/work/workflow_enumerator/anatMRIQCT1w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/MNItpms2t1/mapflow/_MNItpms2t11". | |
| 200228-14:25:04,170 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/ham19006/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/ham19006/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 14:25:04,170 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/ham19006/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/ham19006/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 | |
| 200228-14:25:09,759 nipype.workflow INFO: | |
| [Node] Finished "_MNItpms2t11". | |
| 2020-02-28 14:25:09,759 nipype.workflow:INFO [Node] Finished "_MNItpms2t11". | |
| 200228-14:25:10,165 nipype.workflow INFO: | |
| [Node] Setting-up "_MNItpms2t12" in "/gpfs/scratchfs1/ham19006/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 14:25:10,165 nipype.workflow:INFO [Node] Setting-up "_MNItpms2t12" in "/gpfs/scratchfs1/ham19006/hw3/work/workflow_enumerator/anatMRIQCT1w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/MNItpms2t1/mapflow/_MNItpms2t12". | |
| 200228-14:25:10,168 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/ham19006/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/ham19006/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 14:25:10,168 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/ham19006/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/ham19006/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 | |
| 200228-14:25:15,688 nipype.workflow INFO: | |
| [Node] Finished "_MNItpms2t12". | |
| 2020-02-28 14:25:15,688 nipype.workflow:INFO [Node] Finished "_MNItpms2t12". | |
| 200228-14:25:16,180 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.ComputeIQMs.MNItpms2t1" in "/gpfs/scratchfs1/ham19006/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 14:25:16,180 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.ComputeIQMs.MNItpms2t1" in "/gpfs/scratchfs1/ham19006/hw3/work/workflow_enumerator/anatMRIQCT1w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/MNItpms2t1". | |
| 200228-14:25:16,196 nipype.workflow INFO: | |
| [Node] Setting-up "_MNItpms2t10" in "/gpfs/scratchfs1/ham19006/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 14:25:16,196 nipype.workflow:INFO [Node] Setting-up "_MNItpms2t10" in "/gpfs/scratchfs1/ham19006/hw3/work/workflow_enumerator/anatMRIQCT1w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/MNItpms2t1/mapflow/_MNItpms2t10". | |
| 200228-14:25:16,197 nipype.workflow INFO: | |
| [Node] Cached "_MNItpms2t10" - collecting precomputed outputs | |
| 2020-02-28 14:25:16,197 nipype.workflow:INFO [Node] Cached "_MNItpms2t10" - collecting precomputed outputs | |
| 200228-14:25:16,197 nipype.workflow INFO: | |
| [Node] "_MNItpms2t10" found cached. | |
| 2020-02-28 14:25:16,197 nipype.workflow:INFO [Node] "_MNItpms2t10" found cached. | |
| 200228-14:25:16,198 nipype.workflow INFO: | |
| [Node] Setting-up "_MNItpms2t11" in "/gpfs/scratchfs1/ham19006/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 14:25:16,198 nipype.workflow:INFO [Node] Setting-up "_MNItpms2t11" in "/gpfs/scratchfs1/ham19006/hw3/work/workflow_enumerator/anatMRIQCT1w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/MNItpms2t1/mapflow/_MNItpms2t11". | |
| 200228-14:25:16,199 nipype.workflow INFO: | |
| [Node] Cached "_MNItpms2t11" - collecting precomputed outputs | |
| 2020-02-28 14:25:16,199 nipype.workflow:INFO [Node] Cached "_MNItpms2t11" - collecting precomputed outputs | |
| 200228-14:25:16,199 nipype.workflow INFO: | |
| [Node] "_MNItpms2t11" found cached. | |
| 2020-02-28 14:25:16,199 nipype.workflow:INFO [Node] "_MNItpms2t11" found cached. | |
| 200228-14:25:16,200 nipype.workflow INFO: | |
| [Node] Setting-up "_MNItpms2t12" in "/gpfs/scratchfs1/ham19006/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 14:25:16,200 nipype.workflow:INFO [Node] Setting-up "_MNItpms2t12" in "/gpfs/scratchfs1/ham19006/hw3/work/workflow_enumerator/anatMRIQCT1w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/MNItpms2t1/mapflow/_MNItpms2t12". | |
| 200228-14:25:16,201 nipype.workflow INFO: | |
| [Node] Cached "_MNItpms2t12" - collecting precomputed outputs | |
| 2020-02-28 14:25:16,201 nipype.workflow:INFO [Node] Cached "_MNItpms2t12" - collecting precomputed outputs | |
| 200228-14:25:16,201 nipype.workflow INFO: | |
| [Node] "_MNItpms2t12" found cached. | |
| 2020-02-28 14:25:16,201 nipype.workflow:INFO [Node] "_MNItpms2t12" found cached. | |
| 200228-14:25:16,203 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT1w.ComputeIQMs.MNItpms2t1". | |
| 2020-02-28 14:25:16,203 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT1w.ComputeIQMs.MNItpms2t1". | |
| 200228-14:25:18,194 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.ComputeIQMs.measures" in "/gpfs/scratchfs1/ham19006/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 14:25:18,194 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.ComputeIQMs.measures" in "/gpfs/scratchfs1/ham19006/hw3/work/workflow_enumerator/anatMRIQCT1w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/measures". | |
| 200228-14:25:18,197 nipype.workflow INFO: | |
| [Node] Running "measures" ("mriqc.interfaces.anatomical.StructuralQC") | |
| 2020-02-28 14:25:18,197 nipype.workflow:INFO [Node] Running "measures" ("mriqc.interfaces.anatomical.StructuralQC") | |
| 200228-14:25:31,697 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT1w.ComputeIQMs.measures". | |
| 2020-02-28 14:25:31,697 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT1w.ComputeIQMs.measures". | |
| 200228-14:25:34,347 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.ReportsWorkflow.GenerateReport" in "/gpfs/scratchfs1/ham19006/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 14:25:34,347 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.ReportsWorkflow.GenerateReport" in "/gpfs/scratchfs1/ham19006/hw3/work/workflow_enumerator/anatMRIQCT1w/ReportsWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/GenerateReport". | |
| 200228-14:25:34,352 nipype.workflow INFO: | |
| [Node] Running "GenerateReport" ("nipype.interfaces.utility.wrappers.Function") | |
| 2020-02-28 14:25:34,352 nipype.workflow:INFO [Node] Running "GenerateReport" ("nipype.interfaces.utility.wrappers.Function") | |
| 200228-14:25:34,759 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT1w.ReportsWorkflow.GenerateReport". | |
| 2020-02-28 14:25:34,759 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT1w.ReportsWorkflow.GenerateReport". | |
| 200228-14:25:36,589 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.UploadMetrics" in "/gpfs/scratchfs1/ham19006/hw3/work/workflow_enumerator/anatMRIQCT1w/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/UploadMetrics". | |
| 2020-02-28 14:25:36,589 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT1w.UploadMetrics" in "/gpfs/scratchfs1/ham19006/hw3/work/workflow_enumerator/anatMRIQCT1w/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T1w.nii.gz/UploadMetrics". | |
| 200228-14:25:36,591 nipype.workflow INFO: | |
| [Node] Running "UploadMetrics" ("mriqc.interfaces.webapi.UploadIQMs") | |
| 2020-02-28 14:25:36,591 nipype.workflow:INFO [Node] Running "UploadMetrics" ("mriqc.interfaces.webapi.UploadIQMs") | |
| 200228-14:25:37,185 nipype.interface INFO: | |
| MRIQC Web API: submitting to <https://mriqc.nimh.nih.gov:443/api/v1/T1w> | |
| 2020-02-28 14:25:37,185 nipype.interface:INFO MRIQC Web API: submitting to <https://mriqc.nimh.nih.gov:443/api/v1/T1w> | |
| 200228-14:25:37,334 nipype.interface INFO: | |
| QC metrics successfully uploaded. | |
| 2020-02-28 14:25:37,334 nipype.interface:INFO QC metrics successfully uploaded. | |
| 200228-14:25:37,338 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT1w.UploadMetrics". | |
| 2020-02-28 14:25:37,338 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT1w.UploadMetrics". | |
| 2020-02-28 14:25:53,188 niworkflows:INFO Terminal outputs of initialization saved (/gpfs/scratchfs1/ham19006/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 14:25:53,188 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 14:25:53,191 niworkflows:INFO Retry #1, commandline: | |
| antsRegistration --collapse-output-transforms 1 --dimensionality 3 --float 0 --initial-moving-transform [ /gpfs/scratchfs1/ham19006/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/ham19006/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/ham19006/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/ham19006/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/ham19006/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/ham19006/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/ham19006/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 | |
| 200228-14:26:47,997 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT2w.segmentation". | |
| 2020-02-28 14:26:47,997 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT2w.segmentation". | |
| 200228-14:26:48,409 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.ComputeIQMs.harmonize" in "/gpfs/scratchfs1/ham19006/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 14:26:48,409 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.ComputeIQMs.harmonize" in "/gpfs/scratchfs1/ham19006/hw3/work/workflow_enumerator/anatMRIQCT2w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/harmonize". | |
| 200228-14:26:48,411 nipype.workflow INFO: | |
| [Node] Running "harmonize" ("mriqc.interfaces.anatomical.Harmonize") | |
| 2020-02-28 14:26:48,411 nipype.workflow:INFO [Node] Running "harmonize" ("mriqc.interfaces.anatomical.Harmonize") | |
| 200228-14:26:52,802 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT2w.ComputeIQMs.harmonize". | |
| 2020-02-28 14:26:52,802 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT2w.ComputeIQMs.harmonize". | |
| 2020-02-28 14:29:40,705 niworkflows:INFO Successful spatial normalization (retry #1). | |
| 2020-02-28 14:29:44,120 niworkflows:INFO Report - setting fixed (/gpfs/scratchfs1/ham19006/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/ham19006/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 14:29:44,121 niworkflows:INFO Generating visual report | |
| 200228-14:29:53,118 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT2w.SpatialNormalization.SpatialNormalization". | |
| 2020-02-28 14:29:53,118 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT2w.SpatialNormalization.SpatialNormalization". | |
| 200228-14:29:54,609 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.AirMaskWorkflow.invert_xfm" in "/gpfs/scratchfs1/ham19006/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 14:29:54,609 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.AirMaskWorkflow.invert_xfm" in "/gpfs/scratchfs1/ham19006/hw3/work/workflow_enumerator/anatMRIQCT2w/AirMaskWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/invert_xfm". | |
| 200228-14:29:54,612 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/ham19006/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/ham19006/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 14:29:54,612 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/ham19006/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/ham19006/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 | |
| 200228-14:29:56,603 nipype.workflow INFO: | |
| [Node] Setting-up "_MNItpms2t10" in "/gpfs/scratchfs1/ham19006/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 14:29:56,603 nipype.workflow:INFO [Node] Setting-up "_MNItpms2t10" in "/gpfs/scratchfs1/ham19006/hw3/work/workflow_enumerator/anatMRIQCT2w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/MNItpms2t1/mapflow/_MNItpms2t10". | |
| 200228-14:29:56,604 nipype.workflow INFO: | |
| [Node] Setting-up "_MNItpms2t11" in "/gpfs/scratchfs1/ham19006/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 14:29:56,604 nipype.workflow:INFO [Node] Setting-up "_MNItpms2t11" in "/gpfs/scratchfs1/ham19006/hw3/work/workflow_enumerator/anatMRIQCT2w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/MNItpms2t1/mapflow/_MNItpms2t11". | |
| 200228-14:29:56,606 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/ham19006/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/ham19006/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 14:29:56,606 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/ham19006/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/ham19006/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 | |
| 200228-14:29:56,607 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/ham19006/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/ham19006/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 14:29:56,607 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/ham19006/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/ham19006/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 | |
| 200228-14:30:02,197 nipype.workflow INFO: | |
| [Node] Finished "_MNItpms2t11". | |
| 2020-02-28 14:30:02,197 nipype.workflow:INFO [Node] Finished "_MNItpms2t11". | |
| 200228-14:30:02,224 nipype.workflow INFO: | |
| [Node] Finished "_MNItpms2t10". | |
| 2020-02-28 14:30:02,224 nipype.workflow:INFO [Node] Finished "_MNItpms2t10". | |
| 200228-14:30:02,605 nipype.workflow INFO: | |
| [Node] Setting-up "_MNItpms2t12" in "/gpfs/scratchfs1/ham19006/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 14:30:02,605 nipype.workflow:INFO [Node] Setting-up "_MNItpms2t12" in "/gpfs/scratchfs1/ham19006/hw3/work/workflow_enumerator/anatMRIQCT2w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/MNItpms2t1/mapflow/_MNItpms2t12". | |
| 200228-14:30:02,610 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/ham19006/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/ham19006/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 14:30:02,610 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/ham19006/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/ham19006/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 | |
| 200228-14:30:08,108 nipype.workflow INFO: | |
| [Node] Finished "_MNItpms2t12". | |
| 2020-02-28 14:30:08,108 nipype.workflow:INFO [Node] Finished "_MNItpms2t12". | |
| 200228-14:30:08,613 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.ComputeIQMs.MNItpms2t1" in "/gpfs/scratchfs1/ham19006/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 14:30:08,613 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.ComputeIQMs.MNItpms2t1" in "/gpfs/scratchfs1/ham19006/hw3/work/workflow_enumerator/anatMRIQCT2w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/MNItpms2t1". | |
| 200228-14:30:08,617 nipype.workflow INFO: | |
| [Node] Setting-up "_MNItpms2t10" in "/gpfs/scratchfs1/ham19006/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 14:30:08,617 nipype.workflow:INFO [Node] Setting-up "_MNItpms2t10" in "/gpfs/scratchfs1/ham19006/hw3/work/workflow_enumerator/anatMRIQCT2w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/MNItpms2t1/mapflow/_MNItpms2t10". | |
| 200228-14:30:08,618 nipype.workflow INFO: | |
| [Node] Cached "_MNItpms2t10" - collecting precomputed outputs | |
| 2020-02-28 14:30:08,618 nipype.workflow:INFO [Node] Cached "_MNItpms2t10" - collecting precomputed outputs | |
| 200228-14:30:08,618 nipype.workflow INFO: | |
| [Node] "_MNItpms2t10" found cached. | |
| 2020-02-28 14:30:08,618 nipype.workflow:INFO [Node] "_MNItpms2t10" found cached. | |
| 200228-14:30:08,619 nipype.workflow INFO: | |
| [Node] Setting-up "_MNItpms2t11" in "/gpfs/scratchfs1/ham19006/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 14:30:08,619 nipype.workflow:INFO [Node] Setting-up "_MNItpms2t11" in "/gpfs/scratchfs1/ham19006/hw3/work/workflow_enumerator/anatMRIQCT2w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/MNItpms2t1/mapflow/_MNItpms2t11". | |
| 200228-14:30:08,619 nipype.workflow INFO: | |
| [Node] Cached "_MNItpms2t11" - collecting precomputed outputs | |
| 2020-02-28 14:30:08,619 nipype.workflow:INFO [Node] Cached "_MNItpms2t11" - collecting precomputed outputs | |
| 200228-14:30:08,619 nipype.workflow INFO: | |
| [Node] "_MNItpms2t11" found cached. | |
| 2020-02-28 14:30:08,619 nipype.workflow:INFO [Node] "_MNItpms2t11" found cached. | |
| 200228-14:30:08,620 nipype.workflow INFO: | |
| [Node] Setting-up "_MNItpms2t12" in "/gpfs/scratchfs1/ham19006/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 14:30:08,620 nipype.workflow:INFO [Node] Setting-up "_MNItpms2t12" in "/gpfs/scratchfs1/ham19006/hw3/work/workflow_enumerator/anatMRIQCT2w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/MNItpms2t1/mapflow/_MNItpms2t12". | |
| 200228-14:30:08,621 nipype.workflow INFO: | |
| [Node] Cached "_MNItpms2t12" - collecting precomputed outputs | |
| 2020-02-28 14:30:08,621 nipype.workflow:INFO [Node] Cached "_MNItpms2t12" - collecting precomputed outputs | |
| 200228-14:30:08,621 nipype.workflow INFO: | |
| [Node] "_MNItpms2t12" found cached. | |
| 2020-02-28 14:30:08,621 nipype.workflow:INFO [Node] "_MNItpms2t12" found cached. | |
| 200228-14:30:08,623 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT2w.ComputeIQMs.MNItpms2t1". | |
| 2020-02-28 14:30:08,623 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT2w.ComputeIQMs.MNItpms2t1". | |
| 200228-14:34:17,154 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT2w.AirMaskWorkflow.invert_xfm". | |
| 2020-02-28 14:34:17,154 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT2w.AirMaskWorkflow.invert_xfm". | |
| 200228-14:34:18,879 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.AirMaskWorkflow.ArtifactMask" in "/gpfs/scratchfs1/ham19006/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 14:34:18,879 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.AirMaskWorkflow.ArtifactMask" in "/gpfs/scratchfs1/ham19006/hw3/work/workflow_enumerator/anatMRIQCT2w/AirMaskWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/ArtifactMask". | |
| 200228-14:34:18,887 nipype.workflow INFO: | |
| [Node] Running "ArtifactMask" ("mriqc.interfaces.anatomical.ArtifactMask") | |
| 2020-02-28 14:34:18,887 nipype.workflow:INFO [Node] Running "ArtifactMask" ("mriqc.interfaces.anatomical.ArtifactMask") | |
| 200228-14:34:26,1 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT2w.AirMaskWorkflow.ArtifactMask". | |
| 2020-02-28 14:34:26,001 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT2w.AirMaskWorkflow.ArtifactMask". | |
| 200228-14:34:26,882 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.ComputeIQMs.ComputeQI2" in "/gpfs/scratchfs1/ham19006/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 14:34:26,882 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.ComputeIQMs.ComputeQI2" in "/gpfs/scratchfs1/ham19006/hw3/work/workflow_enumerator/anatMRIQCT2w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/ComputeQI2". | |
| 200228-14:34:26,885 nipype.workflow INFO: | |
| [Node] Running "ComputeQI2" ("mriqc.interfaces.anatomical.ComputeQI2") | |
| 2020-02-28 14:34:26,885 nipype.workflow:INFO [Node] Running "ComputeQI2" ("mriqc.interfaces.anatomical.ComputeQI2") | |
| 200228-14:34:26,888 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.ComputeIQMs.measures" in "/gpfs/scratchfs1/ham19006/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 14:34:26,888 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.ComputeIQMs.measures" in "/gpfs/scratchfs1/ham19006/hw3/work/workflow_enumerator/anatMRIQCT2w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/measures". | |
| 200228-14:34:26,891 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.ComputeIQMs.provenance" in "/gpfs/scratchfs1/ham19006/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 14:34:26,891 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.ComputeIQMs.provenance" in "/gpfs/scratchfs1/ham19006/hw3/work/workflow_enumerator/anatMRIQCT2w/ComputeIQMs/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/provenance". | |
| 200228-14:34:26,892 nipype.workflow INFO: | |
| [Node] Running "measures" ("mriqc.interfaces.anatomical.StructuralQC") | |
| 2020-02-28 14:34:26,892 nipype.workflow:INFO [Node] Running "measures" ("mriqc.interfaces.anatomical.StructuralQC") | |
| 200228-14:34:26,894 nipype.workflow INFO: | |
| [Node] Running "provenance" ("nipype.interfaces.utility.wrappers.Function") | |
| 2020-02-28 14:34:26,894 nipype.workflow:INFO [Node] Running "provenance" ("nipype.interfaces.utility.wrappers.Function") | |
| 200228-14:34:27,175 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT2w.ComputeIQMs.provenance". | |
| 2020-02-28 14:34:27,175 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT2w.ComputeIQMs.provenance". | |
| 200228-14:34:39,866 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT2w.ComputeIQMs.measures". | |
| 2020-02-28 14:34:39,866 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT2w.ComputeIQMs.measures". | |
| 200228-14:35:13,923 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT2w.ComputeIQMs.ComputeQI2". | |
| 2020-02-28 14:35:13,923 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT2w.ComputeIQMs.ComputeQI2". | |
| 200228-14:35:16,926 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.ReportsWorkflow.GenerateReport" in "/gpfs/scratchfs1/ham19006/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 14:35:16,926 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.ReportsWorkflow.GenerateReport" in "/gpfs/scratchfs1/ham19006/hw3/work/workflow_enumerator/anatMRIQCT2w/ReportsWorkflow/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/GenerateReport". | |
| 200228-14:35:16,927 nipype.workflow INFO: | |
| [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.UploadMetrics" in "/gpfs/scratchfs1/ham19006/hw3/work/workflow_enumerator/anatMRIQCT2w/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/UploadMetrics". | |
| 2020-02-28 14:35:16,927 nipype.workflow:INFO [Node] Setting-up "workflow_enumerator.anatMRIQCT2w.UploadMetrics" in "/gpfs/scratchfs1/ham19006/hw3/work/workflow_enumerator/anatMRIQCT2w/_in_file_..data..sub-01..ses-01..anat..sub-01_ses-01_T2w.nii.gz/UploadMetrics". | |
| 200228-14:35:16,928 nipype.workflow INFO: | |
| [Node] Running "GenerateReport" ("nipype.interfaces.utility.wrappers.Function") | |
| 2020-02-28 14:35:16,928 nipype.workflow:INFO [Node] Running "GenerateReport" ("nipype.interfaces.utility.wrappers.Function") | |
| 200228-14:35:16,929 nipype.workflow INFO: | |
| [Node] Running "UploadMetrics" ("mriqc.interfaces.webapi.UploadIQMs") | |
| 2020-02-28 14:35:16,929 nipype.workflow:INFO [Node] Running "UploadMetrics" ("mriqc.interfaces.webapi.UploadIQMs") | |
| 200228-14:35:17,208 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT2w.ReportsWorkflow.GenerateReport". | |
| 2020-02-28 14:35:17,208 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT2w.ReportsWorkflow.GenerateReport". | |
| 200228-14:35:17,285 nipype.interface INFO: | |
| MRIQC Web API: submitting to <https://mriqc.nimh.nih.gov:443/api/v1/T2w> | |
| 2020-02-28 14:35:17,285 nipype.interface:INFO MRIQC Web API: submitting to <https://mriqc.nimh.nih.gov:443/api/v1/T2w> | |
| 200228-14:35:17,418 nipype.interface INFO: | |
| QC metrics successfully uploaded. | |
| 2020-02-28 14:35:17,418 nipype.interface:INFO QC metrics successfully uploaded. | |
| 200228-14:35:17,421 nipype.workflow INFO: | |
| [Node] Finished "workflow_enumerator.anatMRIQCT2w.UploadMetrics". | |
| 2020-02-28 14:35:17,421 nipype.workflow:INFO [Node] Finished "workflow_enumerator.anatMRIQCT2w.UploadMetrics". | |
| 2020-02-28 14:35:20,938 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 14:35:21,127 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 14:35:21,144 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 14:35:21,144 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() | |