Summary of what happened:
I am trying to run fMRIPrep with the --use-syn-sdc flag but it does not look like it was applied.
Command used (and if a helper script was used, a link to the helper script or the command generated):
apptainer run --cleanenv \
-B /media/mpasternak/ADATA-1TB/GENFI_fMRI_ForceSynSDC:/data \
-B /media/mpasternak/ADATA-1TB/GENFI_fMRI_ForceSynSDC/derivatives/fmriprep:/output \
-B /tmp/sub-GRN007ForceSynSDCm9s2wrne:/work \
-B /tmp/fs_sub-GRN007ForceSynSDC__o4qel3k0:/output/sourcedata/freesurfer \
-B /home/mpasternak/freesurfer/.license:/opt/freesurfer/license.txt:ro \
-B /home/mpasternak/.cache/templateflow \
/home/mpasternak/apps/fmriprep-latest.simg \
/data \
/output \
participant \
-w /work \
--participant-label sub-GRN007ForceSynSDC \
--omp-nthreads 24 \
--fs-license-file /opt/freesurfer/license.txt \
--fs-subjects-dir /output/sourcedata/freesurfer \
--cifti-output \
--random-seed 42 \
--use-syn-sdc \
--ignore fieldmaps \
--force-syn \
--longitudinal
Version:
24.1.1
Environment (Docker, Singularity / Apptainer, custom installation):
Apptainer
Data formatted according to a validatable standard? Please provide the output of the validator:
It is BIDS compatible:
╰$ bids-validator .
bids-validator@1.14.10
(node:137755) [DEP0040] DeprecationWarning: The `punycode` module is deprecated. Please use a userland alternative instead.
(Use `node --trace-deprecation ...` to show where the warning was created)
(node:137755) Warning: Closing directory handle on garbage collection
This dataset appears to be BIDS compatible.
Summary: Available Tasks: Available Modalities:
16 Files, 65.45MB rest MRI
1 - Subject
2 - Sessions
If you have any questions, please post on https://neurostars.org/tags/bids.
Relevant log outputs (up to 20 lines):
No errors occur and the pipeline exits without errors (fMRIPrep still outputs to both stdout and stderr as captured by Python’s subprocess.Popen…is that intentional?)
sub-GRN007ForceSynSDC_fmriprep.log.txt (244.4 KB)
sub-GRN007ForceSynSDC_fmriprep.err.txt (348.6 KB)
sub-GRN007ForceSynSDC.html.txt (77.9 KB)
No sign of the SDC workflow being run.
It does clearly recognize that it should proceed with the fieldmapless correction:
2024-11-13 17:20:12,796 [ INFO] Option "--ignore fieldmaps" was set, but either "--use-syn-sdc" or "--force-syn" were given, so fieldmap-less estimation will be executed.
But that’s the only mention of SDC I see in the logs and no mention of skipping it.
Screenshots / relevant information:
Let’s get a layout of the land, so to speak:
.
├── derivatives
│ └── fmriprep
│ ├── logs
│ │ ├── CITATION.bib
│ │ ├── CITATION.html
│ │ ├── CITATION.md
│ │ ├── CITATION.tex
│ │ ├── python_fmriprep_run.log
│ │ ├── sub-GRN007ForceSynSDC_fmriprep.err
│ │ └── sub-GRN007ForceSynSDC_fmriprep.log
│ ├── scripts
│ ├── sourcedata
│ │ └── freesurfer
│ ├── sub-GRN007ForceSynSDC
│ │ ├── anat
│ │ ├── figures
│ │ ├── log
│ │ ├── ses-V01
│ │ └── ses-V02
│ ├── dataset_description.json
│ ├── desc-aparcaseg_dseg.tsv
│ ├── desc-aseg_dseg.tsv
│ └── sub-GRN007ForceSynSDC.html
├── sub-GRN007ForceSynSDC
│ ├── ses-V01
│ │ ├── anat
│ │ │ ├── sub-GRN007ForceSynSDC_ses-V01_acq-Philips3Tt1_rec-Real_T1w.json
│ │ │ ├── sub-GRN007ForceSynSDC_ses-V01_acq-Philips3Tt1_rec-Real_T1w.nii.gz
│ │ │ ├── sub-GRN007ForceSynSDC_ses-V01_acq-Philips3Tt2_rec-Real_T2w.json
│ │ │ └── sub-GRN007ForceSynSDC_ses-V01_acq-Philips3Tt2_rec-Real_T2w.nii.gz
│ │ └── func
│ │ ├── sub-GRN007ForceSynSDC_ses-V01_task-rest_acq-Philips3T_bold.json
│ │ └── sub-GRN007ForceSynSDC_ses-V01_task-rest_acq-Philips3T_bold.nii.gz
│ └── ses-V02
│ ├── anat
│ │ ├── sub-GRN007ForceSynSDC_ses-V02_acq-Philips3Tt1_rec-Real_T1w.json
│ │ ├── sub-GRN007ForceSynSDC_ses-V02_acq-Philips3Tt1_rec-Real_T1w.nii.gz
│ │ ├── sub-GRN007ForceSynSDC_ses-V02_acq-Philips3Tt2_rec-Real_T2w.json
│ │ └── sub-GRN007ForceSynSDC_ses-V02_acq-Philips3Tt2_rec-Real_T2w.nii.gz
│ └── func
│ ├── sub-GRN007ForceSynSDC_ses-V02_task-rest_acq-Philips3T_bold.json
│ └── sub-GRN007ForceSynSDC_ses-V02_task-rest_acq-Philips3T_bold.nii.gz
├── dataset_description.json
├── participants.tsv
└── README.md
Would appreciate the thoughts of anyone on the fMRIPrep team.
Thanks!