Hi @ejdavid,
SDC seems to run fine with the data you sent. Here is the preamble I get:
241021-10:57:46,76 nipype.workflow IMPORTANT:
Building fMRIPrep's workflow:
* BIDS dataset path: /om2/scratch/tmp/smeisler/support_proc/sub-055/data.
* Participant list: ['055'].
* Run identifier: 20241021-105726_760e9952-7880-4b42-a20f-54341bdf987c.
* Output spaces: fsnative.
* Pre-run FreeSurfer's SUBJECTS_DIR: /om2/scratch/tmp/smeisler/support_proc/sub-055/data/derivatives/freesurfer.
2024-10-21 10:57:46,076 [IMPORTANT] Building fMRIPrep's workflow:
* BIDS dataset path: /om2/scratch/tmp/smeisler/support_proc/sub-055/data.
* Participant list: ['055'].
* Run identifier: 20241021-105726_760e9952-7880-4b42-a20f-54341bdf987c.
* Output spaces: fsnative.
* Pre-run FreeSurfer's SUBJECTS_DIR: /om2/scratch/tmp/smeisler/support_proc/sub-055/data/derivatives/freesurfer.
241021-10:57:46,764 nipype.workflow INFO:
ANAT Stage 1: Adding template workflow
2024-10-21 10:57:46,764 [ INFO] ANAT Stage 1: Adding template workflow
2024-10-21 10:57:47,025 [ WARNING] WARNING: 'locale.getdefaultlocale' is deprecated and slated for removal in Python 3.15. Use setlocale(), getencoding() and getlocale() instead.
2024-10-21 10:57:47,025 [ WARNING] WARNING: 'locale.getdefaultlocale' is deprecated and slated for removal in Python 3.15. Use setlocale(), getencoding() and getlocale() instead.
241021-10:57:47,269 nipype.workflow INFO:
ANAT Stage 2: Preparing brain extraction workflow
2024-10-21 10:57:47,269 [ INFO] ANAT Stage 2: Preparing brain extraction workflow
241021-10:57:47,349 nipype.workflow INFO:
ANAT Stage 3: Preparing segmentation workflow
2024-10-21 10:57:47,349 [ INFO] ANAT Stage 3: Preparing segmentation workflow
241021-10:57:47,354 nipype.workflow INFO:
ANAT Stage 4: Preparing normalization workflow for ['MNI152NLin2009cAsym']
2024-10-21 10:57:47,354 [ INFO] ANAT Stage 4: Preparing normalization workflow for ['MNI152NLin2009cAsym']
241021-10:57:47,363 nipype.workflow INFO:
ANAT Stage 5: Preparing surface reconstruction workflow
2024-10-21 10:57:47,363 [ INFO] ANAT Stage 5: Preparing surface reconstruction workflow
241021-10:57:47,381 nipype.workflow INFO:
ANAT Stage 6: Preparing mask refinement workflow
2024-10-21 10:57:47,381 [ INFO] ANAT Stage 6: Preparing mask refinement workflow
241021-10:57:47,383 nipype.workflow INFO:
ANAT No T2w images provided - skipping Stage 7
2024-10-21 10:57:47,383 [ INFO] ANAT No T2w images provided - skipping Stage 7
241021-10:57:47,383 nipype.workflow INFO:
ANAT Stage 8: Creating GIFTI surfaces for ['white', 'pial', 'midthickness', 'sphere_reg', 'sphere']
2024-10-21 10:57:47,383 [ INFO] ANAT Stage 8: Creating GIFTI surfaces for ['white', 'pial', 'midthickness', 'sphere_reg', 'sphere']
241021-10:57:47,399 nipype.workflow INFO:
ANAT Stage 8: Creating GIFTI metrics for ['thickness', 'sulc']
2024-10-21 10:57:47,399 [ INFO] ANAT Stage 8: Creating GIFTI metrics for ['thickness', 'sulc']
241021-10:57:47,406 nipype.workflow INFO:
ANAT Stage 8a: Creating cortical ribbon mask
2024-10-21 10:57:47,406 [ INFO] ANAT Stage 8a: Creating cortical ribbon mask
241021-10:57:47,409 nipype.workflow INFO:
ANAT Stage 9: Creating fsLR registration sphere
2024-10-21 10:57:47,409 [ INFO] ANAT Stage 9: Creating fsLR registration sphere
241021-10:57:47,413 nipype.workflow INFO:
ANAT Stage 10: Creating MSM-Sulc registration sphere
2024-10-21 10:57:47,413 [ INFO] ANAT Stage 10: Creating MSM-Sulc registration sphere
241021-10:57:48,287 nipype.workflow INFO:
B0 field inhomogeneity map will be estimated with the following 2 estimator(s): [<EstimatorType.PEPOLAR: 2>, <EstimatorType.PEPOLAR: 2>].
2024-10-21 10:57:48,287 [ INFO] B0 field inhomogeneity map will be estimated with the following 2 estimator(s): [<EstimatorType.PEPOLAR: 2>, <EstimatorType.PEPOLAR: 2>].
241021-10:57:48,361 nipype.workflow INFO:
Setting-up fieldmap "fmap_19" (EstimatorType.PEPOLAR) with <sub-055_acq-mbep2d19mm_dir-AP_epi.nii.gz, sub-055_acq-mbep2d19mm_dir-PA_epi.nii.gz>
2024-10-21 10:57:48,361 [ INFO] Setting-up fieldmap "fmap_19" (EstimatorType.PEPOLAR) with <sub-055_acq-mbep2d19mm_dir-AP_epi.nii.gz, sub-055_acq-mbep2d19mm_dir-PA_epi.nii.gz>
241021-10:57:48,377 nipype.workflow INFO:
Setting-up fieldmap "fmap_14" (EstimatorType.PEPOLAR) with <sub-055_acq-mbep2d14mm_dir-AP_epi.nii.gz, sub-055_acq-mbep2d14mm_dir-PA_epi.nii.gz>
2024-10-21 10:57:48,377 [ INFO] Setting-up fieldmap "fmap_14" (EstimatorType.PEPOLAR) with <sub-055_acq-mbep2d14mm_dir-AP_epi.nii.gz, sub-055_acq-mbep2d14mm_dir-PA_epi.nii.gz>
241021-10:57:48,496 nipype.workflow INFO:
No single-band-reference found for sub-055_task-cloudySCR_acq-ep2d19mm_run-01_echo-1_bold.nii.gz.
2024-10-21 10:57:48,496 [ INFO] No single-band-reference found for sub-055_task-cloudySCR_acq-ep2d19mm_run-01_echo-1_bold.nii.gz.
241021-10:57:48,576 nipype.workflow INFO:
Stage 1: Adding HMC boldref workflow
2024-10-21 10:57:48,576 [ INFO] Stage 1: Adding HMC boldref workflow
241021-10:57:48,583 nipype.workflow INFO:
Stage 2: Adding motion correction workflow
2024-10-21 10:57:48,583 [ INFO] Stage 2: Adding motion correction workflow
241021-10:57:48,591 nipype.workflow INFO:
Stage 3: Adding coregistration boldref workflow
2024-10-21 10:57:48,591 [ INFO] Stage 3: Adding coregistration boldref workflow
2024-10-21 10:57:48,592 [ WARNING] WARNING: niworkflows.interfaces.nibabel.BinaryDilation is deprecated in favor of
niworkflows.interfaces.morphology.BinaryDilation. Please validate that
interface for your use case and switch.
241021-10:57:48,797 nipype.workflow IMPORTANT:
Generating T2* map and optimally combined ME-EPI time series.
2024-10-21 10:57:48,797 [IMPORTANT] Generating T2* map and optimally combined ME-EPI time series.
241021-10:57:48,956 nipype.workflow INFO:
No single-band-reference found for sub-055_task-cloudy_acq-ep2d19mm_run-01_echo-1_bold.nii.gz.
2024-10-21 10:57:48,956 [ INFO] No single-band-reference found for sub-055_task-cloudy_acq-ep2d19mm_run-01_echo-1_bold.nii.gz.
241021-10:57:49,22 nipype.workflow INFO:
Stage 1: Adding HMC boldref workflow
2024-10-21 10:57:49,022 [ INFO] Stage 1: Adding HMC boldref workflow
241021-10:57:49,27 nipype.workflow INFO:
Stage 2: Adding motion correction workflow
2024-10-21 10:57:49,027 [ INFO] Stage 2: Adding motion correction workflow
241021-10:57:49,31 nipype.workflow INFO:
Stage 3: Adding coregistration boldref workflow
2024-10-21 10:57:49,031 [ INFO] Stage 3: Adding coregistration boldref workflow
2024-10-21 10:57:49,032 [ WARNING] WARNING: niworkflows.interfaces.nibabel.BinaryDilation is deprecated in favor of
niworkflows.interfaces.morphology.BinaryDilation. Please validate that
interface for your use case and switch.
241021-10:57:49,234 nipype.workflow IMPORTANT:
Generating T2* map and optimally combined ME-EPI time series.
2024-10-21 10:57:49,234 [IMPORTANT] Generating T2* map and optimally combined ME-EPI time series.
241021-10:57:49,376 nipype.workflow INFO:
No single-band-reference found for sub-055_task-fmri_acq-3D12mm_dir-PA_run-01_bold.nii.gz.
2024-10-21 10:57:49,376 [ INFO] No single-band-reference found for sub-055_task-fmri_acq-3D12mm_dir-PA_run-01_bold.nii.gz.
241021-10:57:49,438 nipype.workflow INFO:
Stage 1: Adding HMC boldref workflow
2024-10-21 10:57:49,438 [ INFO] Stage 1: Adding HMC boldref workflow
241021-10:57:49,443 nipype.workflow INFO:
Stage 2: Adding motion correction workflow
2024-10-21 10:57:49,443 [ INFO] Stage 2: Adding motion correction workflow
241021-10:57:49,447 nipype.workflow INFO:
Stage 3: Adding coregistration boldref workflow
2024-10-21 10:57:49,447 [ INFO] Stage 3: Adding coregistration boldref workflow
2024-10-21 10:57:49,448 [ WARNING] WARNING: niworkflows.interfaces.nibabel.BinaryDilation is deprecated in favor of
niworkflows.interfaces.morphology.BinaryDilation. Please validate that
interface for your use case and switch.
241021-10:57:49,633 nipype.workflow INFO:
No single-band-reference found for sub-055_task-fmri_acq-3D12mm_run-01_bold.nii.gz.
2024-10-21 10:57:49,633 [ INFO] No single-band-reference found for sub-055_task-fmri_acq-3D12mm_run-01_bold.nii.gz.
241021-10:57:49,695 nipype.workflow INFO:
Stage 1: Adding HMC boldref workflow
2024-10-21 10:57:49,695 [ INFO] Stage 1: Adding HMC boldref workflow
241021-10:57:49,700 nipype.workflow INFO:
Stage 2: Adding motion correction workflow
2024-10-21 10:57:49,700 [ INFO] Stage 2: Adding motion correction workflow
241021-10:57:49,704 nipype.workflow INFO:
Stage 3: Adding coregistration boldref workflow
2024-10-21 10:57:49,704 [ INFO] Stage 3: Adding coregistration boldref workflow
2024-10-21 10:57:49,705 [ WARNING] WARNING: niworkflows.interfaces.nibabel.BinaryDilation is deprecated in favor of
niworkflows.interfaces.morphology.BinaryDilation. Please validate that
interface for your use case and switch.
241021-10:57:49,873 nipype.workflow INFO:
No single-band-reference found for sub-055_task-fmri_acq-3D12mm_run-02_bold.nii.gz.
2024-10-21 10:57:49,873 [ INFO] No single-band-reference found for sub-055_task-fmri_acq-3D12mm_run-02_bold.nii.gz.
241021-10:57:49,935 nipype.workflow INFO:
Stage 1: Adding HMC boldref workflow
2024-10-21 10:57:49,935 [ INFO] Stage 1: Adding HMC boldref workflow
241021-10:57:49,940 nipype.workflow INFO:
Stage 2: Adding motion correction workflow
2024-10-21 10:57:49,940 [ INFO] Stage 2: Adding motion correction workflow
241021-10:57:49,944 nipype.workflow INFO:
Stage 3: Adding coregistration boldref workflow
2024-10-21 10:57:49,944 [ INFO] Stage 3: Adding coregistration boldref workflow
2024-10-21 10:57:49,945 [ WARNING] WARNING: niworkflows.interfaces.nibabel.BinaryDilation is deprecated in favor of
niworkflows.interfaces.morphology.BinaryDilation. Please validate that
interface for your use case and switch.
241021-10:57:50,948 nipype.workflow INFO:
No single-band-reference found for sub-055_task-presentSCR_acq-ep2d19mm_run-01_echo-1_bold.nii.gz.
2024-10-21 10:57:50,948 [ INFO] No single-band-reference found for sub-055_task-presentSCR_acq-ep2d19mm_run-01_echo-1_bold.nii.gz.
241021-10:57:51,13 nipype.workflow INFO:
Stage 1: Adding HMC boldref workflow
2024-10-21 10:57:51,013 [ INFO] Stage 1: Adding HMC boldref workflow
241021-10:57:51,18 nipype.workflow INFO:
Stage 2: Adding motion correction workflow
2024-10-21 10:57:51,018 [ INFO] Stage 2: Adding motion correction workflow
241021-10:57:51,22 nipype.workflow INFO:
Stage 3: Adding coregistration boldref workflow
2024-10-21 10:57:51,022 [ INFO] Stage 3: Adding coregistration boldref workflow
2024-10-21 10:57:51,023 [ WARNING] WARNING: niworkflows.interfaces.nibabel.BinaryDilation is deprecated in favor of
niworkflows.interfaces.morphology.BinaryDilation. Please validate that
interface for your use case and switch.
241021-10:57:51,222 nipype.workflow IMPORTANT:
Generating T2* map and optimally combined ME-EPI time series.
2024-10-21 10:57:51,222 [IMPORTANT] Generating T2* map and optimally combined ME-EPI time series.
241021-10:57:51,370 nipype.workflow INFO:
No single-band-reference found for sub-055_task-present_acq-ep2d19mm_run-01_echo-1_bold.nii.gz.
2024-10-21 10:57:51,370 [ INFO] No single-band-reference found for sub-055_task-present_acq-ep2d19mm_run-01_echo-1_bold.nii.gz.
241021-10:57:51,437 nipype.workflow INFO:
Stage 1: Adding HMC boldref workflow
2024-10-21 10:57:51,437 [ INFO] Stage 1: Adding HMC boldref workflow
241021-10:57:51,442 nipype.workflow INFO:
Stage 2: Adding motion correction workflow
2024-10-21 10:57:51,442 [ INFO] Stage 2: Adding motion correction workflow
241021-10:57:51,445 nipype.workflow INFO:
Stage 3: Adding coregistration boldref workflow
2024-10-21 10:57:51,445 [ INFO] Stage 3: Adding coregistration boldref workflow
2024-10-21 10:57:51,446 [ WARNING] WARNING: niworkflows.interfaces.nibabel.BinaryDilation is deprecated in favor of
niworkflows.interfaces.morphology.BinaryDilation. Please validate that
interface for your use case and switch.
241021-10:57:51,648 nipype.workflow IMPORTANT:
Generating T2* map and optimally combined ME-EPI time series.
2024-10-21 10:57:51,648 [IMPORTANT] Generating T2* map and optimally combined ME-EPI time series.
241021-10:57:51,799 nipype.workflow INFO:
No single-band-reference found for sub-055_task-rest_acq-ep2d19mm_run-01_echo-1_bold.nii.gz.
2024-10-21 10:57:51,799 [ INFO] No single-band-reference found for sub-055_task-rest_acq-ep2d19mm_run-01_echo-1_bold.nii.gz.
241021-10:57:51,866 nipype.workflow INFO:
Stage 1: Adding HMC boldref workflow
2024-10-21 10:57:51,866 [ INFO] Stage 1: Adding HMC boldref workflow
241021-10:57:51,871 nipype.workflow INFO:
Stage 2: Adding motion correction workflow
2024-10-21 10:57:51,871 [ INFO] Stage 2: Adding motion correction workflow
241021-10:57:51,874 nipype.workflow INFO:
Stage 3: Adding coregistration boldref workflow
2024-10-21 10:57:51,874 [ INFO] Stage 3: Adding coregistration boldref workflow
2024-10-21 10:57:51,875 [ WARNING] WARNING: niworkflows.interfaces.nibabel.BinaryDilation is deprecated in favor of
niworkflows.interfaces.morphology.BinaryDilation. Please validate that
interface for your use case and switch.
241021-10:57:52,73 nipype.workflow IMPORTANT:
Generating T2* map and optimally combined ME-EPI time series.
2024-10-21 10:57:52,073 [IMPORTANT] Generating T2* map and optimally combined ME-EPI time series.
241021-10:57:52,223 nipype.workflow INFO:
No single-band-reference found for sub-055_task-rest_acq-megre14mm_dir-PA_run-01_echo-1_bold.nii.gz.
2024-10-21 10:57:52,223 [ INFO] No single-band-reference found for sub-055_task-rest_acq-megre14mm_dir-PA_run-01_echo-1_bold.nii.gz.
241021-10:57:52,288 nipype.workflow INFO:
Stage 1: Adding HMC boldref workflow
2024-10-21 10:57:52,288 [ INFO] Stage 1: Adding HMC boldref workflow
241021-10:57:52,293 nipype.workflow INFO:
Stage 2: Adding motion correction workflow
2024-10-21 10:57:52,293 [ INFO] Stage 2: Adding motion correction workflow
241021-10:57:52,297 nipype.workflow INFO:
Stage 3: Adding coregistration boldref workflow
2024-10-21 10:57:52,297 [ INFO] Stage 3: Adding coregistration boldref workflow
2024-10-21 10:57:52,298 [ WARNING] WARNING: niworkflows.interfaces.nibabel.BinaryDilation is deprecated in favor of
niworkflows.interfaces.morphology.BinaryDilation. Please validate that
interface for your use case and switch.
241021-10:57:52,502 nipype.workflow IMPORTANT:
Generating T2* map and optimally combined ME-EPI time series.
2024-10-21 10:57:52,502 [IMPORTANT] Generating T2* map and optimally combined ME-EPI time series.
241021-10:57:52,653 nipype.workflow INFO:
No single-band-reference found for sub-055_task-rest_acq-megre14mm_run-02_echo-1_bold.nii.gz.
2024-10-21 10:57:52,653 [ INFO] No single-band-reference found for sub-055_task-rest_acq-megre14mm_run-02_echo-1_bold.nii.gz.
241021-10:57:52,720 nipype.workflow INFO:
Stage 1: Adding HMC boldref workflow
2024-10-21 10:57:52,720 [ INFO] Stage 1: Adding HMC boldref workflow
241021-10:57:52,725 nipype.workflow INFO:
Stage 2: Adding motion correction workflow
2024-10-21 10:57:52,725 [ INFO] Stage 2: Adding motion correction workflow
241021-10:57:52,729 nipype.workflow INFO:
Stage 3: Adding coregistration boldref workflow
2024-10-21 10:57:52,729 [ INFO] Stage 3: Adding coregistration boldref workflow
2024-10-21 10:57:52,730 [ WARNING] WARNING: niworkflows.interfaces.nibabel.BinaryDilation is deprecated in favor of
niworkflows.interfaces.morphology.BinaryDilation. Please validate that
interface for your use case and switch.
241021-10:57:52,936 nipype.workflow IMPORTANT:
Generating T2* map and optimally combined ME-EPI time series.
2024-10-21 10:57:52,936 [IMPORTANT] Generating T2* map and optimally combined ME-EPI time series.
2024-10-21 10:57:55,785 [ WARNING] WARNING: SOCKS support in urllib3 requires the installation of optional dependencies: specifically, PySocks. For more information, see https://urllib3.readthedocs.io/en/latest/advanced-usage.html#socks-proxies
2024-10-21 10:57:55,927 [ WARNING] WARNING: Niworkflows will be deprecating reporting in favor of a standalone library "nireports".
2024-10-21 10:57:55,996 [ WARNING] WARNING: Niworkflows will be deprecating visualizations in favor of a standalone library "nireports".
241021-10:57:57,876 nipype.workflow INFO:
fMRIPrep workflow graph with 2094 nodes built successfully.
2024-10-21 10:57:57,876 [ INFO] fMRIPrep workflow graph with 2094 nodes built successfully.
2024-10-21 10:58:01,037 [ WARNING] WARNING: Niworkflows will be deprecating reporting in favor of a standalone library "nireports".
2024-10-21 10:58:01,104 [ WARNING] WARNING: Niworkflows will be deprecating visualizations in favor of a standalone library "nireports".
2024-10-21 10:58:10,276 [ WARNING] WARNING: SOCKS support in urllib3 requires the installation of optional dependencies: specifically, PySocks. For more information, see https://urllib3.readthedocs.io/en/latest/advanced-usage.html#socks-proxies
2024-10-21 10:58:10,414 [ WARNING] WARNING: Niworkflows will be deprecating reporting in favor of a standalone library "nireports".
2024-10-21 10:58:10,482 [ WARNING] WARNING: Niworkflows will be deprecating visualizations in favor of a standalone library "nireports".
2024-10-21 10:58:13,253 [ WARNING] WARNING: sentry_sdk.configure_scope is deprecated and will be removed in the next major version. Please consult our migration guide to learn how to migrate to the new API: https://docs.sentry.io/platforms/python/migration/1.x-to-2.x#scope-configuring
241021-10:58:14,209 nipype.workflow IMPORTANT:
fMRIPrep started!
2024-10-21 10:58:14,209 [IMPORTANT] fMRIPrep started!
Note that the fieldmaps are set up after the ANAT staging. I used the same set of arguments as you.
Best,
Steven
