fMRIPrep Not Using Fmaps

Steven · October 21, 2024, 2:59pm

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

ejdavid · October 21, 2024, 3:53pm

Sorry, I’m quite confused here. The outputs I am getting from fMRIPrep seem to indicate that SDC is not being applied.

I’m also not seeing the notification in my run for 'Setting-up fieldmap “fmap_14” in my output like I am in yours.

(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>

Instead, mine just simply skips the field map part that yours has included.

	 ANAT Stage 10: Creating MSM-Sulc registration sphere
2024-10-21 18:45:21,966 [    INFO] ANAT Stage 10: Creating MSM-Sulc registration sphere
241021-18:45:24,0 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 18:45:24,000 [    INFO] No single-band-reference found for sub-055_task-cloudySCR_acq-ep2d19mm_run-01_echo-1_bold.nii.gz.
241021-18:45:24,120 nipype.workflow INFO:
	 Stage 1: Adding HMC boldref workflow
2024-10-21 18:45:24,120 [    INFO] Stage 1: Adding HMC boldref workflow

Am I missing something here? What could this mean?

Steven · October 21, 2024, 9:09pm

I’m sorry I’m not sure what to tell you. The data worked fine for me using a similar command, without touching the data. The only difference I could think of is that I used 24.1.0rc2 (just because it was what I had immediately on hand) and did not --skip-bids-validation.

ejdavid · October 22, 2024, 3:33pm

Well this is incredibly strange. I tried it with bids validation enabled and fmriprep 24.1.0rc2 and I’m still having the same issue. If it works for you and not me, there must be something different about how docker is being called or maybe a version of something related. Is there anything you can think of that might be different here? Would you be able to share your script of how you are calling fmriprep?

Steven · October 22, 2024, 5:57pm

#!/bin/bash -l 
#SBATCH --time=8:00:00 # 8 hours
#SBATCH --mem=64GB
#SBATCH --cpus-per-task=32
#SBATCH -J func_proc

### Load Apptainer/Singularity
module add openmind8/apptainer/1.1.7

### Define memory limits for fmriprep
mem_mb="63500"
nprocs="32"
omp_nprocs="16"

### Make outputs read/writable for group
umask 0002
set -eu # Code will stop on errors

### Define versions and paths
fmriprep_version=24.1.0rc2
freesurfer_version=7.4.1
path_to_imgs=/om2/user/smeisler/
fmriprep_IMG=${path_to_imgs}/fmriprep_${fmriprep_version}.img
templateflow_dir="/om2/user/smeisler/.cache/templateflow/"
export APPTAINERENV_TEMPLATEFLOW_HOME=$templateflow_dir

### Import arguments from job submission script
args=($@)
subjs=(${args[@]:1})
bids_dir=$1

### Locate fs_license
fs_license=$bids_dir/code/license.txt

### index slurm array to grab subject ID
subject=${subjs[${SLURM_ARRAY_TASK_ID}]}

### Define and create scratch directory (temporary single-subject BIDS directory in scratch space)
scratch=/om2/scratch/tmp/$(whoami)/support_proc/$subject/ # assign working directory
mkdir -p ${scratch}/data/derivatives/fmriprep/
mkdir -p ${scratch}/data/derivatives/freesurfer/

### assign output directory
output_dir=${bids_dir}/derivatives/

### Copy single-subject data and minimal files to scratch
cp -n $bids_dir/*.json ${scratch}/data/
cp -n $bids_dir/README ${scratch}/data/
cp -f $bids_dir/.bidsignore ${scratch}/data/
cp -nr $bids_dir/$subject/ ${scratch}/data/
cp -n $fs_license ${scratch}/license.txt

### If FreeSurfer outputs already exist, move them to scratch
if [ -d ${output_dir}/freesurfer_${freesurfer_version}/$subject ]
then cp -rn ${output_dir}/freesurfer_${freesurfer_version}/$subject/ ${scratch}/data/derivatives/freesurfer/
fi

### Remove FreeSurfer temp files that stop recon-all
rm -f ${scratch}/data/derivatives/freesurfer/$subject/scripts/*Running*


### Do fMRIPrep
cd $scratch

fmriprep_cmd="singularity run -e --containall -B ${scratch},${templateflow_dir} $fmriprep_IMG --participant_label ${subject:4} -w $scratch --fs-license-file ${scratch}/license.txt --fs-subjects-dir ${scratch}/data/derivatives/freesurfer/ --mem_mb ${mem_mb} --nprocs ${nprocs} --omp-nthreads ${omp_nprocs}  --skull-strip-t1w force --me-output-echos --output-spaces fsnative --ignore slicetiming --low-mem $scratch/data $scratch/data/derivatives/fmriprep participant"

echo "Submitted fmriprep job for: ${subject}"
echo $'Command :\n'${fmriprep_cmd}
${fmriprep_cmd}

### Copy data back to final destination from scratch space
mkdir -p ${output_dir}/fmriprep_${fmriprep_version}/
mkdir -p ${output_dir}/freesurfer_${freesurfer_version}/
cp -rn $scratch/data/derivatives/fmriprep/$subject ${output_dir}/fmriprep_${fmriprep_version}/
cp -n $scratch/data/derivatives/fmriprep/*.* ${output_dir}/fmriprep_${fmriprep_version}/
cp -n $scratch/data/derivatives/fmriprep/.bidsignore ${output_dir}/fmriprep_${fmriprep_version}/
cp -rn $scratch/data/derivatives/freesurfer/$subject ${output_dir}/freesurfer_${freesurfer_version}/
cp -rn $scratch/data/derivatives/freesurfer/fsaverage ${output_dir}/freesurfer_${freesurfer_version}/

ejdavid · October 24, 2024, 5:04pm

I’ve tried averything I can think of to get this working. The only real difference I can see is that you used Singularity instead of Docker (which shouldn’t be the difference, I assume?)

Is there any possibility that because I ran participants before using the proper tags in the .json files, it is defaulting to some older template version where fmaps are not being applied? I’ve tried deleting the work folders but I’m really stumped at what else it could be at this point.

Steven · October 24, 2024, 5:37pm

Hi @ejdavid,

Even if you’re not deleting work folders, that shouldn’t be a problem, as the workflow is built early on using the JSONS, so fmriprep would be able to detect if the workflow is different (e.g., SDC nodes are added) and work accordingly. Deleting the work dir is also safe.

Unfortunately I think I’ve done everything I can from a far to help. Will you eventually be moving to an HPC, which tend to use Singularity?

Best,
Steven

ejdavid · October 24, 2024, 10:28pm

I’ve also now tried it in singularity with the following command:

#!/bin/bash -l 

### Define memory limits for fMRIPrep
mem_mb="63500"
nprocs="32"
omp_nprocs="16"

### Make outputs read/writable for group
umask 0002
set -eu # Code will stop on errors

### Define versions and paths
fmriprep_version="24.1.0rc2"
freesurfer_version="7.4.1"
bids_dir="/lbc/lbc1/derivatives/brainstem_funk/BIDS_DAY2"
output_dir="/lbc/lbc1/derivatives/brainstem_funk/fmriprep"
fmriprep_IMG="/lbc/lbc1/derivatives/brainstem_funk/scripts/fmriprep_${fmriprep_version}.sif"
templateflow_dir="/lbc/lbc1/derivatives/brainstem_funk/templateflow"
fs_license="/lbc/lbc1/derivatives/brainstem_funk/license.txt"
export fs_license="/lbc/lbc1/derivatives/brainstem_funk/license.txt"
export SINGULARITYENV_TEMPLATEFLOW_HOME=/templateflow



echo "TemplateFlow Directory: $templateflow_dir"
echo "FMRIPrep Image: $fmriprep_IMG"

### Check if subject number argument is provided
if [ $# -ne 1 ]; then
    echo "Usage: $0 <subject_number>"
    exit 1
fi

### Import subject ID from command line
subject=$1
echo "Processing Subject ID: $subject"
echo "BIDS Directory: $bids_dir"


### Do fMRIPrep directly on the original data without copying
echo "Running fMRIPrep command..."

fmriprep_cmd="singularity run -e --containall \
    -B /lbc/lbc1/derivatives/brainstem_funk/BIDS_DAY2,\
/lbc/lbc1/derivatives/brainstem_funk/fmriprep,\
/lbc/lbc1/derivatives/brainstem_funk/templateflow_cache:/templateflow,\
/lbc/lbc1/derivatives/brainstem_funk:/derivatives \
    /lbc/lbc1/derivatives/brainstem_funk/scripts/fmriprep_${fmriprep_version}.sif \
    --skip-bids-validation --participant_label ${subject} \
    --fs-license-file /derivatives/license.txt \
    --fs-subjects-dir /derivatives/fmriprep/freesurfer_${freesurfer_version}/ \
    --mem_mb ${mem_mb} --nprocs ${nprocs} --omp-nthreads ${omp_nprocs} \
    --skull-strip-t1w force --me-output-echos \
    --output-spaces fsnative --ignore slicetiming --low-mem \
    ${bids_dir} ${output_dir}/fmriprep_${fmriprep_version}/ participant"



echo "Submitted fmriprep job for: ${subject}"
echo -e "Command:\n${fmriprep_cmd}"
${fmriprep_cmd}

As you can see, no mention of the field maps:

241024-18:23:22,130 nipype.workflow IMPORTANT:
	 Running fMRIPrep version 24.1.0rc2

         License NOTICE ##################################################
         fMRIPrep 24.1.0rc2
         Copyright The NiPreps Developers.
         
         This product includes software developed by
         the NiPreps Community (https://nipreps.org/).
         
         Portions of this software were developed at the Department of
         Psychology at Stanford University, Stanford, CA, US.
         
         This software is also distributed as a Docker container image.
         The bootstrapping file for the image ("Dockerfile") is licensed
         under the MIT License.
         
         This software may be distributed through an add-on package called
         "Docker Wrapper" that is under the BSD 3-clause License.
         #################################################################
2024-10-24 18:23:22,130 [IMPORTANT] Running fMRIPrep version 24.1.0rc2

         License NOTICE ##################################################
         fMRIPrep 24.1.0rc2
         Copyright The NiPreps Developers.
         
         This product includes software developed by
         the NiPreps Community (https://nipreps.org/).
         
         Portions of this software were developed at the Department of
         Psychology at Stanford University, Stanford, CA, US.
         
         This software is also distributed as a Docker container image.
         The bootstrapping file for the image ("Dockerfile") is licensed
         under the MIT License.
         
         This software may be distributed through an add-on package called
         "Docker Wrapper" that is under the BSD 3-clause License.
         #################################################################
241024-18:23:22,373 nipype.workflow IMPORTANT:
	 Building fMRIPrep's workflow:
           * BIDS dataset path: /lbc/lbc1/derivatives/brainstem_funk/BIDS_DAY2.
           * Participant list: ['055'].
           * Run identifier: 20241024-182244_a46db071-a695-452b-890b-57381ee57a83.
           * Output spaces: fsnative.
           * Pre-run FreeSurfer's SUBJECTS_DIR: /derivatives/fmriprep/freesurfer_7.4.1.
2024-10-24 18:23:22,373 [IMPORTANT] Building fMRIPrep's workflow:
           * BIDS dataset path: /lbc/lbc1/derivatives/brainstem_funk/BIDS_DAY2.
           * Participant list: ['055'].
           * Run identifier: 20241024-182244_a46db071-a695-452b-890b-57381ee57a83.
           * Output spaces: fsnative.
           * Pre-run FreeSurfer's SUBJECTS_DIR: /derivatives/fmriprep/freesurfer_7.4.1.
Downloading https://templateflow.s3.amazonaws.com/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-01_T1w.nii.gz
100%|███████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 13.7M/13.7M [00:02<00:00, 5.68MB/s]
Downloading https://templateflow.s3.amazonaws.com/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-01_desc-brain_mask.nii.gz
100%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 160k/160k [00:00<00:00, 3.98MB/s]
241024-18:23:28,790 nipype.workflow INFO:
	 ANAT Stage 1: Adding template workflow
2024-10-24 18:23:28,790 [    INFO] ANAT Stage 1: Adding template workflow
2024-10-24 18:23:33,317 [ WARNING] WARNING: 'locale.getdefaultlocale' is deprecated and slated for removal in Python 3.15. Use setlocale(), getencoding() and getlocale() instead.
2024-10-24 18:23:33,318 [ WARNING] WARNING: 'locale.getdefaultlocale' is deprecated and slated for removal in Python 3.15. Use setlocale(), getencoding() and getlocale() instead.
241024-18:23:33,605 nipype.workflow INFO:
	 ANAT Stage 2: Preparing brain extraction workflow
2024-10-24 18:23:33,605 [    INFO] ANAT Stage 2: Preparing brain extraction workflow
Downloading https://templateflow.s3.amazonaws.com/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_T1w.nii.gz
100%|███████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 32.4M/32.4M [00:00<00:00, 34.6MB/s]
Downloading https://templateflow.s3.amazonaws.com/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_label-brain_probseg.nii.gz
100%|███████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 2.59M/2.59M [00:00<00:00, 16.3MB/s]
Downloading https://templateflow.s3.amazonaws.com/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_desc-BrainCerebellumExtraction_mask.nii.gz
100%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 265k/265k [00:00<00:00, 4.88MB/s]
Downloading https://templateflow.s3.amazonaws.com/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_label-WM_probseg.nii.gz
100%|███████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 4.06M/4.06M [00:00<00:00, 18.7MB/s]
Downloading https://templateflow.s3.amazonaws.com/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_label-BS_probseg.nii.gz
100%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 447k/447k [00:00<00:00, 8.13MB/s]
241024-18:23:36,764 nipype.workflow INFO:
	 ANAT Stage 3: Preparing segmentation workflow
2024-10-24 18:23:36,764 [    INFO] ANAT Stage 3: Preparing segmentation workflow
241024-18:23:36,779 nipype.workflow INFO:
	 ANAT Stage 4: Preparing normalization workflow for ['MNI152NLin2009cAsym']
2024-10-24 18:23:36,779 [    INFO] ANAT Stage 4: Preparing normalization workflow for ['MNI152NLin2009cAsym']
241024-18:23:36,825 nipype.workflow INFO:
	 ANAT Stage 5: Preparing surface reconstruction workflow
2024-10-24 18:23:36,825 [    INFO] ANAT Stage 5: Preparing surface reconstruction workflow
241024-18:23:36,855 nipype.workflow INFO:
	 ANAT Stage 6: Preparing mask refinement workflow
2024-10-24 18:23:36,855 [    INFO] ANAT Stage 6: Preparing mask refinement workflow
241024-18:23:36,859 nipype.workflow INFO:
	 ANAT No T2w images provided - skipping Stage 7
2024-10-24 18:23:36,859 [    INFO] ANAT No T2w images provided - skipping Stage 7
241024-18:23:36,859 nipype.workflow INFO:
	 ANAT Stage 8: Creating GIFTI surfaces for ['white', 'pial', 'midthickness', 'sphere_reg', 'sphere']
2024-10-24 18:23:36,859 [    INFO] ANAT Stage 8: Creating GIFTI surfaces for ['white', 'pial', 'midthickness', 'sphere_reg', 'sphere']
241024-18:23:36,885 nipype.workflow INFO:
	 ANAT Stage 8: Creating GIFTI metrics for ['thickness', 'sulc']
2024-10-24 18:23:36,885 [    INFO] ANAT Stage 8: Creating GIFTI metrics for ['thickness', 'sulc']
241024-18:23:36,895 nipype.workflow INFO:
	 ANAT Stage 8a: Creating cortical ribbon mask
2024-10-24 18:23:36,895 [    INFO] ANAT Stage 8a: Creating cortical ribbon mask
241024-18:23:36,900 nipype.workflow INFO:
	 ANAT Stage 9: Creating fsLR registration sphere
2024-10-24 18:23:36,900 [    INFO] ANAT Stage 9: Creating fsLR registration sphere
241024-18:23:36,912 nipype.workflow INFO:
	 ANAT Stage 10: Creating MSM-Sulc registration sphere
2024-10-24 18:23:36,912 [    INFO] ANAT Stage 10: Creating MSM-Sulc registration sphere
241024-18:23:37,337 nipype.workflow INFO:
	 No single-band-reference found for sub-055_task-cloudySCR_acq-ep2d19mm_run-01_echo-1_bold.nii.gz.
2024-10-24 18:23:37,337 [    INFO] No single-band-reference found for sub-055_task-cloudySCR_acq-ep2d19mm_run-01_echo-1_bold.nii.gz.
241024-18:23:37,645 nipype.workflow INFO:
	 Stage 1: Adding HMC boldref workflow
2024-10-24 18:23:37,645 [    INFO] Stage 1: Adding HMC boldref workflow
241024-18:23:37,656 nipype.workflow INFO:
	 Stage 2: Adding motion correction workflow
2024-10-24 18:23:37,656 [    INFO] Stage 2: Adding motion correction workflow
241024-18:23:37,669 nipype.workflow INFO:
	 Stage 3: Adding coregistration boldref workflow
2024-10-24 18:23:37,669 [    INFO] Stage 3: Adding coregistration boldref workflow
2024-10-24 18:23:37,671 [ 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.

Interestingly, the fmaps still aren’t being processed. I don’t know what to do at this point. It’s imperative I get these rolling…is there someone you can think of that I could contact about this? It has to be something related to my system if it works fine for you.

Steven · October 24, 2024, 10:32pm

I didn’t skip BIDS validation and also made a temporary BIDS directory with only the one subject folder you sent me (55 I believe). Can you try doing that?

Steven · October 24, 2024, 10:58pm

You don’t happen to have a .bidsignore file with fmaps specified, do you?

ejdavid · October 24, 2024, 11:00pm

I just ran this on one participant (55, the one I sent to you) in a temporary BIDS directory using the following code:

#!/bin/bash -l

### Define memory limits for fMRIPrep
mem_mb="63500"
nprocs="32"
omp_nprocs="16"

### Make outputs read/writable for group
umask 0002
set -eu  # Code will stop on errors

### Define versions and paths
fmriprep_version="24.1.0rc2"
freesurfer_version="7.4.1"
bids_dir="/lbc/lbc1/derivatives/brainstem_funk/BIDS_DAY2"
output_dir="/lbc/lbc1/derivatives/brainstem_funk/fmriprep"
fmriprep_IMG="/lbc/lbc1/derivatives/brainstem_funk/scripts/fmriprep_${fmriprep_version}.sif"
templateflow_dir="/lbc/lbc1/derivatives/brainstem_funk/templateflow_cache"
fs_license="/lbc/lbc1/derivatives/brainstem_funk/license.txt"

# Set TemplateFlow home inside the container
export SINGULARITYENV_TEMPLATEFLOW_HOME=/templateflow

echo "TemplateFlow Directory: $templateflow_dir"
echo "FMRIPrep Image: $fmriprep_IMG"

### Check if subject number argument is provided
if [ $# -ne 1 ]; then
    echo "Usage: $0 <subject_number>"
    exit 1
fi

### Import subject ID from command line
subject=$1
echo "Processing Subject ID: $subject"
echo "BIDS Directory: $bids_dir"

### Create a temporary working directory (scratch space)
scratch_dir="/lbc/lbc1/scratch/tmp/$(whoami)/support_proc/$subject"
mkdir -p "${scratch_dir}/data"
mkdir -p "${scratch_dir}/license"
mkdir -p "${scratch_dir}/output"

### Copy necessary files to the temporary BIDS directory
echo "Copying necessary BIDS files to scratch directory..."
cp -r "${bids_dir}/dataset_description.json" "${scratch_dir}/data/"
cp -r "${bids_dir}/participants.json" "${scratch_dir}/data/" 2>/dev/null || true
cp -r "${bids_dir}/README" "${scratch_dir}/data/" 2>/dev/null || true
cp -r "${bids_dir}/CHANGES" "${scratch_dir}/data/" 2>/dev/null || true
cp -r "${bids_dir}/.bidsignore" "${scratch_dir}/data/" 2>/dev/null || true
cp -r "${bids_dir}/code" "${scratch_dir}/data/" 2>/dev/null || true

# Copy only the specific subject's data
cp -r "${bids_dir}/sub-${subject}" "${scratch_dir}/data/"

# Copy the FreeSurfer license file
cp "${fs_license}" "${scratch_dir}/license/license.txt"

### Adjust output directory within scratch
output_scratch="${scratch_dir}/output"

### Do fMRIPrep
echo "Running fMRIPrep..."

fmriprep_cmd="singularity run -e --containall \
    -B ${scratch_dir}/data:/data,\
${scratch_dir}/license:/license,\
${output_scratch}:/out,\
${templateflow_dir}:/templateflow \
    ${fmriprep_IMG} \
    /data /out participant \
    --participant-label ${subject} \
    --fs-license-file /license/license.txt \
    --fs-subjects-dir /out/freesurfer_${freesurfer_version} \
    --mem_mb ${mem_mb} --nprocs ${nprocs} --omp-nthreads ${omp_nprocs} \
    --skull-strip-t1w force --me-output-echos \
    --output-spaces fsnative \
    --ignore slicetiming \
    --low-mem"

echo "Submitted fMRIPrep job for: ${subject}"
echo -e "Command:\n${fmriprep_cmd}"
eval ${fmriprep_cmd}

### Copy results back to the original output directory
echo "Copying results back to the original output directory..."
mkdir -p "${output_dir}/fmriprep_${fmriprep_version}"
mkdir -p "${output_dir}/freesurfer_${freesurfer_version}"

cp -r "${output_scratch}/fmriprep/sub-${subject}" "${output_dir}/fmriprep_${fmriprep_version}/"
cp -r "${output_scratch}/freesurfer_${freesurfer_version}/sub-${subject}" "${output_dir}/freesurfer_${freesurfer_version}/"

### Clean up scratch directory (optional)
# rm -rf "${scratch_dir}"

echo "Processing for subject ${subject} completed."

I got the following output:

	 Running fMRIPrep version 24.1.0rc2

         License NOTICE ##################################################
         fMRIPrep 24.1.0rc2
         Copyright The NiPreps Developers.
         
         This product includes software developed by
         the NiPreps Community (https://nipreps.org/).
         
         Portions of this software were developed at the Department of
         Psychology at Stanford University, Stanford, CA, US.
         
         This software is also distributed as a Docker container image.
         The bootstrapping file for the image ("Dockerfile") is licensed
         under the MIT License.
         
         This software may be distributed through an add-on package called
         "Docker Wrapper" that is under the BSD 3-clause License.
         #################################################################
2024-10-24 18:52:24,506 [IMPORTANT] Running fMRIPrep version 24.1.0rc2

         License NOTICE ##################################################
         fMRIPrep 24.1.0rc2
         Copyright The NiPreps Developers.
         
         This product includes software developed by
         the NiPreps Community (https://nipreps.org/).
         
         Portions of this software were developed at the Department of
         Psychology at Stanford University, Stanford, CA, US.
         
         This software is also distributed as a Docker container image.
         The bootstrapping file for the image ("Dockerfile") is licensed
         under the MIT License.
         
         This software may be distributed through an add-on package called
         "Docker Wrapper" that is under the BSD 3-clause License.
         #################################################################
241024-18:52:24,758 nipype.workflow IMPORTANT:
	 Building fMRIPrep's workflow:
           * BIDS dataset path: /data.
           * Participant list: ['055'].
           * Run identifier: 20241024-185205_59b52861-d6cc-428d-8b0a-6c3186059044.
           * Output spaces: fsnative.
           * Pre-run FreeSurfer's SUBJECTS_DIR: /out/freesurfer_7.4.1.
2024-10-24 18:52:24,758 [IMPORTANT] Building fMRIPrep's workflow:
           * BIDS dataset path: /data.
           * Participant list: ['055'].
           * Run identifier: 20241024-185205_59b52861-d6cc-428d-8b0a-6c3186059044.
           * Output spaces: fsnative.
           * Pre-run FreeSurfer's SUBJECTS_DIR: /out/freesurfer_7.4.1.
241024-18:52:25,292 nipype.workflow INFO:
	 ANAT Stage 1: Adding template workflow
2024-10-24 18:52:25,292 [    INFO] ANAT Stage 1: Adding template workflow
2024-10-24 18:52:25,611 [ WARNING] WARNING: 'locale.getdefaultlocale' is deprecated and slated for removal in Python 3.15. Use setlocale(), getencoding() and getlocale() instead.
2024-10-24 18:52:25,611 [ WARNING] WARNING: 'locale.getdefaultlocale' is deprecated and slated for removal in Python 3.15. Use setlocale(), getencoding() and getlocale() instead.
241024-18:52:25,820 nipype.workflow INFO:
	 ANAT Stage 2: Preparing brain extraction workflow
2024-10-24 18:52:25,820 [    INFO] ANAT Stage 2: Preparing brain extraction workflow
241024-18:52:25,904 nipype.workflow INFO:
	 ANAT Stage 3: Preparing segmentation workflow
2024-10-24 18:52:25,904 [    INFO] ANAT Stage 3: Preparing segmentation workflow
241024-18:52:25,909 nipype.workflow INFO:
	 ANAT Stage 4: Preparing normalization workflow for ['MNI152NLin2009cAsym']
2024-10-24 18:52:25,909 [    INFO] ANAT Stage 4: Preparing normalization workflow for ['MNI152NLin2009cAsym']
241024-18:52:25,922 nipype.workflow INFO:
	 ANAT Stage 5: Preparing surface reconstruction workflow
2024-10-24 18:52:25,922 [    INFO] ANAT Stage 5: Preparing surface reconstruction workflow
241024-18:52:25,941 nipype.workflow INFO:
	 ANAT Stage 6: Preparing mask refinement workflow
2024-10-24 18:52:25,941 [    INFO] ANAT Stage 6: Preparing mask refinement workflow
241024-18:52:25,944 nipype.workflow INFO:
	 ANAT No T2w images provided - skipping Stage 7
2024-10-24 18:52:25,944 [    INFO] ANAT No T2w images provided - skipping Stage 7
241024-18:52:25,944 nipype.workflow INFO:
	 ANAT Stage 8: Creating GIFTI surfaces for ['white', 'pial', 'midthickness', 'sphere_reg', 'sphere']
2024-10-24 18:52:25,944 [    INFO] ANAT Stage 8: Creating GIFTI surfaces for ['white', 'pial', 'midthickness', 'sphere_reg', 'sphere']
241024-18:52:25,961 nipype.workflow INFO:
	 ANAT Stage 8: Creating GIFTI metrics for ['thickness', 'sulc']
2024-10-24 18:52:25,961 [    INFO] ANAT Stage 8: Creating GIFTI metrics for ['thickness', 'sulc']
241024-18:52:25,967 nipype.workflow INFO:
	 ANAT Stage 8a: Creating cortical ribbon mask
2024-10-24 18:52:25,967 [    INFO] ANAT Stage 8a: Creating cortical ribbon mask
241024-18:52:25,971 nipype.workflow INFO:
	 ANAT Stage 9: Creating fsLR registration sphere
2024-10-24 18:52:25,971 [    INFO] ANAT Stage 9: Creating fsLR registration sphere
241024-18:52:25,975 nipype.workflow INFO:
	 ANAT Stage 10: Creating MSM-Sulc registration sphere
2024-10-24 18:52:25,975 [    INFO] ANAT Stage 10: Creating MSM-Sulc registration sphere
241024-18:52:26,248 nipype.workflow INFO:
	 No single-band-reference found for sub-055_task-cloudySCR_acq-ep2d19mm_run-01_echo-1_bold.nii.gz.
2024-10-24 18:52:26,248 [    INFO] No single-band-reference found for sub-055_task-cloudySCR_acq-ep2d19mm_run-01_echo-1_bold.nii.gz.
241024-18:52:26,344 nipype.workflow INFO:
	 Stage 1: Adding HMC boldref workflow
2024-10-24 18:52:26,344 [    INFO] Stage 1: Adding HMC boldref workflow
241024-18:52:26,351 nipype.workflow INFO:
	 Stage 2: Adding motion correction workflow
2024-10-24 18:52:26,351 [    INFO] Stage 2: Adding motion correction workflow
241024-18:52:26,359 nipype.workflow INFO:
	 Stage 3: Adding coregistration boldref workflow
2024-10-24 18:52:26,359 [    INFO] Stage 3: Adding coregistration boldref workflow
2024-10-24 18:52:26,360 [ 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.

241024-18:52:26,644 nipype.workflow IMPORTANT:
	 Generating T2* map and optimally combined ME-EPI time series.
2024-10-24 18:52:26,644 [IMPORTANT] Generating T2* map and optimally combined ME-EPI time series.
241024-18:52:26,822 nipype.workflow INFO:
	 No single-band-reference found for sub-055_task-cloudy_acq-ep2d19mm_run-01_echo-1_bold.nii.gz.
2024-10-24 18:52:26,822 [    INFO] No single-band-reference found for sub-055_task-cloudy_acq-ep2d19mm_run-01_echo-1_bold.nii.gz.
241024-18:52:26,901 nipype.workflow INFO:
	 Stage 1: Adding HMC boldref workflow
2024-10-24 18:52:26,901 [    INFO] Stage 1: Adding HMC boldref workflow
241024-18:52:26,907 nipype.workflow INFO:
	 Stage 2: Adding motion correction workflow
2024-10-24 18:52:26,907 [    INFO] Stage 2: Adding motion correction workflow
241024-18:52:26,911 nipype.workflow INFO:
	 Stage 3: Adding coregistration boldref workflow
2024-10-24 18:52:26,911 [    INFO] Stage 3: Adding coregistration boldref workflow
2024-10-24 18:52:26,912 [ 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.

241024-18:52:27,212 nipype.workflow IMPORTANT:
	 Generating T2* map and optimally combined ME-EPI time series.
2024-10-24 18:52:27,212 [IMPORTANT] Generating T2* map and optimally combined ME-EPI time series.
241024-18:52:27,389 nipype.workflow INFO:
	 No single-band-reference found for sub-055_task-fmri_acq-3D12mm_dir-PA_run-01_bold.nii.gz.
2024-10-24 18:52:27,389 [    INFO] No single-band-reference found for sub-055_task-fmri_acq-3D12mm_dir-PA_run-01_bold.nii.gz.
241024-18:52:27,471 nipype.workflow INFO:
	 Stage 1: Adding HMC boldref workflow
2024-10-24 18:52:27,471 [    INFO] Stage 1: Adding HMC boldref workflow
241024-18:52:27,477 nipype.workflow INFO:
	 Stage 2: Adding motion correction workflow
2024-10-24 18:52:27,477 [    INFO] Stage 2: Adding motion correction workflow
241024-18:52:27,482 nipype.workflow INFO:
	 Stage 3: Adding coregistration boldref workflow
2024-10-24 18:52:27,482 [    INFO] Stage 3: Adding coregistration boldref workflow
2024-10-24 18:52:27,483 [ 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.

241024-18:52:27,838 nipype.workflow INFO:
	 No single-band-reference found for sub-055_task-fmri_acq-3D12mm_run-01_bold.nii.gz.
2024-10-24 18:52:27,838 [    INFO] No single-band-reference found for sub-055_task-fmri_acq-3D12mm_run-01_bold.nii.gz.
241024-18:52:27,918 nipype.workflow INFO:
	 Stage 1: Adding HMC boldref workflow
2024-10-24 18:52:27,918 [    INFO] Stage 1: Adding HMC boldref workflow
241024-18:52:27,924 nipype.workflow INFO:
	 Stage 2: Adding motion correction workflow
2024-10-24 18:52:27,924 [    INFO] Stage 2: Adding motion correction workflow
241024-18:52:27,928 nipype.workflow INFO:
	 Stage 3: Adding coregistration boldref workflow
2024-10-24 18:52:27,928 [    INFO] Stage 3: Adding coregistration boldref workflow
2024-10-24 18:52:27,929 [ 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.

241024-18:52:28,205 nipype.workflow INFO:
	 No single-band-reference found for sub-055_task-fmri_acq-3D12mm_run-02_bold.nii.gz.
2024-10-24 18:52:28,205 [    INFO] No single-band-reference found for sub-055_task-fmri_acq-3D12mm_run-02_bold.nii.gz.
241024-18:52:28,289 nipype.workflow INFO:
	 Stage 1: Adding HMC boldref workflow
2024-10-24 18:52:28,289 [    INFO] Stage 1: Adding HMC boldref workflow
241024-18:52:28,296 nipype.workflow INFO:
	 Stage 2: Adding motion correction workflow
2024-10-24 18:52:28,296 [    INFO] Stage 2: Adding motion correction workflow
241024-18:52:28,300 nipype.workflow INFO:
	 Stage 3: Adding coregistration boldref workflow
2024-10-24 18:52:28,300 [    INFO] Stage 3: Adding coregistration boldref workflow
2024-10-24 18:52:28,301 [ 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.

241024-18:52:28,504 nipype.workflow INFO:
	 No single-band-reference found for sub-055_task-presentSCR_acq-ep2d19mm_run-01_echo-1_bold.nii.gz.
2024-10-24 18:52:28,504 [    INFO] No single-band-reference found for sub-055_task-presentSCR_acq-ep2d19mm_run-01_echo-1_bold.nii.gz.
241024-18:52:28,586 nipype.workflow INFO:
	 Stage 1: Adding HMC boldref workflow
2024-10-24 18:52:28,586 [    INFO] Stage 1: Adding HMC boldref workflow
241024-18:52:28,592 nipype.workflow INFO:
	 Stage 2: Adding motion correction workflow
2024-10-24 18:52:28,592 [    INFO] Stage 2: Adding motion correction workflow
241024-18:52:28,596 nipype.workflow INFO:
	 Stage 3: Adding coregistration boldref workflow
2024-10-24 18:52:28,596 [    INFO] Stage 3: Adding coregistration boldref workflow
2024-10-24 18:52:28,597 [ 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.

241024-18:52:28,929 nipype.workflow IMPORTANT:
	 Generating T2* map and optimally combined ME-EPI time series.
2024-10-24 18:52:28,929 [IMPORTANT] Generating T2* map and optimally combined ME-EPI time series.
241024-18:52:29,73 nipype.workflow INFO:
	 No single-band-reference found for sub-055_task-present_acq-ep2d19mm_run-01_echo-1_bold.nii.gz.
2024-10-24 18:52:29,073 [    INFO] No single-band-reference found for sub-055_task-present_acq-ep2d19mm_run-01_echo-1_bold.nii.gz.
241024-18:52:29,153 nipype.workflow INFO:
	 Stage 1: Adding HMC boldref workflow
2024-10-24 18:52:29,153 [    INFO] Stage 1: Adding HMC boldref workflow
241024-18:52:29,159 nipype.workflow INFO:
	 Stage 2: Adding motion correction workflow
2024-10-24 18:52:29,159 [    INFO] Stage 2: Adding motion correction workflow
241024-18:52:29,164 nipype.workflow INFO:
	 Stage 3: Adding coregistration boldref workflow
2024-10-24 18:52:29,164 [    INFO] Stage 3: Adding coregistration boldref workflow
2024-10-24 18:52:29,165 [ 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.

241024-18:52:29,476 nipype.workflow IMPORTANT:
	 Generating T2* map and optimally combined ME-EPI time series.
2024-10-24 18:52:29,476 [IMPORTANT] Generating T2* map and optimally combined ME-EPI time series.
241024-18:52:29,646 nipype.workflow INFO:
	 No single-band-reference found for sub-055_task-rest_acq-ep2d19mm_run-01_echo-1_bold.nii.gz.
2024-10-24 18:52:29,646 [    INFO] No single-band-reference found for sub-055_task-rest_acq-ep2d19mm_run-01_echo-1_bold.nii.gz.
241024-18:52:29,730 nipype.workflow INFO:
	 Stage 1: Adding HMC boldref workflow
2024-10-24 18:52:29,730 [    INFO] Stage 1: Adding HMC boldref workflow
241024-18:52:29,736 nipype.workflow INFO:
	 Stage 2: Adding motion correction workflow
2024-10-24 18:52:29,736 [    INFO] Stage 2: Adding motion correction workflow
241024-18:52:29,741 nipype.workflow INFO:
	 Stage 3: Adding coregistration boldref workflow
2024-10-24 18:52:29,741 [    INFO] Stage 3: Adding coregistration boldref workflow
2024-10-24 18:52:29,741 [ 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.

241024-18:52:30,35 nipype.workflow IMPORTANT:
	 Generating T2* map and optimally combined ME-EPI time series.
2024-10-24 18:52:30,035 [IMPORTANT] Generating T2* map and optimally combined ME-EPI time series.
241024-18:52:30,205 nipype.workflow INFO:
	 No single-band-reference found for sub-055_task-rest_acq-megre14mm_dir-PA_run-01_echo-1_bold.nii.gz.
2024-10-24 18:52:30,205 [    INFO] No single-band-reference found for sub-055_task-rest_acq-megre14mm_dir-PA_run-01_echo-1_bold.nii.gz.
241024-18:52:30,287 nipype.workflow INFO:
	 Stage 1: Adding HMC boldref workflow
2024-10-24 18:52:30,287 [    INFO] Stage 1: Adding HMC boldref workflow
241024-18:52:30,292 nipype.workflow INFO:
	 Stage 2: Adding motion correction workflow
2024-10-24 18:52:30,292 [    INFO] Stage 2: Adding motion correction workflow
241024-18:52:30,296 nipype.workflow INFO:
	 Stage 3: Adding coregistration boldref workflow
2024-10-24 18:52:30,296 [    INFO] Stage 3: Adding coregistration boldref workflow
2024-10-24 18:52:30,297 [ 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.

241024-18:52:30,588 nipype.workflow IMPORTANT:
	 Generating T2* map and optimally combined ME-EPI time series.
2024-10-24 18:52:30,588 [IMPORTANT] Generating T2* map and optimally combined ME-EPI time series.
241024-18:52:30,776 nipype.workflow INFO:
	 No single-band-reference found for sub-055_task-rest_acq-megre14mm_run-02_echo-1_bold.nii.gz.
2024-10-24 18:52:30,776 [    INFO] No single-band-reference found for sub-055_task-rest_acq-megre14mm_run-02_echo-1_bold.nii.gz.
241024-18:52:30,859 nipype.workflow INFO:
	 Stage 1: Adding HMC boldref workflow
2024-10-24 18:52:30,859 [    INFO] Stage 1: Adding HMC boldref workflow
241024-18:52:30,865 nipype.workflow INFO:
	 Stage 2: Adding motion correction workflow
2024-10-24 18:52:30,865 [    INFO] Stage 2: Adding motion correction workflow
241024-18:52:30,869 nipype.workflow INFO:
	 Stage 3: Adding coregistration boldref workflow
2024-10-24 18:52:30,869 [    INFO] Stage 3: Adding coregistration boldref workflow
2024-10-24 18:52:30,870 [ 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.

241024-18:52:31,147 nipype.workflow IMPORTANT:
	 Generating T2* map and optimally combined ME-EPI time series.
2024-10-24 18:52:31,147 [IMPORTANT] Generating T2* map and optimally combined ME-EPI time series.
2024-10-24 18:52:33,876 [ 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
2024-10-24 18:52:33,994 [ WARNING] WARNING: Niworkflows will be deprecating reporting in favor of a standalone library "nireports".
2024-10-24 18:52:34,060 [ WARNING] WARNING: Niworkflows will be deprecating visualizations in favor of a standalone library "nireports".
241024-18:52:35,332 nipype.workflow INFO:
	 fMRIPrep workflow graph with 1820 nodes built successfully.
2024-10-24 18:52:35,332 [    INFO] fMRIPrep workflow graph with 1820 nodes built successfully.
2024-10-24 18:52:38,367 [ WARNING] WARNING: Niworkflows will be deprecating reporting in favor of a standalone library "nireports".
2024-10-24 18:52:38,433 [ WARNING] WARNING: Niworkflows will be deprecating visualizations in favor of a standalone library "nireports".
2024-10-24 18:52:47,646 [ 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
2024-10-24 18:52:47,991 [ WARNING] WARNING: Niworkflows will be deprecating reporting in favor of a standalone library "nireports".
2024-10-24 18:52:48,064 [ WARNING] WARNING: Niworkflows will be deprecating visualizations in favor of a standalone library "nireports".
2024-10-24 18:52:55,168 [ 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
241024-18:52:57,137 nipype.workflow IMPORTANT:
	 fMRIPrep started!
2024-10-24 18:52:57,137 [IMPORTANT] fMRIPrep started!

Field maps still appear not to be used.

No .bidsignore file anywhere.

ejdavid · October 28, 2024, 3:37pm

Ended up solving this problem with a seemingly trivial fix.

Added “DatasetType”: “raw” to the dataset.description.json and it is working fine now. Hopefully this will end up helping someone else avoid the same issue.

Thanks again for the time and assistance with this!