con / con/mechababs

fmriprep outputs: invitation for feedback

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decision pipeline:fmriprep
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Python
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Description

We currently provide these args.

## `anat`

```bash
singularity run \
-B "${PWD}" \
--containall \
--pwd "${PWD}" \
-B $JOB_TMP:/tmp \
-B /templateflow:/templateflow \
-B /license.txt:/SGLR/FREESURFER_HOME/license.txt \
--env TEMPLATEFLOW_HOME=/templateflow \
"containers/.datalad/environments/bids-fmriprep/image" \
"${PWD}/sourcedata/raw" \
"${PWD}/outputs/fMRIPrep-25.2.5+anat" \
participant \
-w .git/tmp/wkdir \
--anat-only \
--output-spaces MNI152NLin2009cAsym:res-2 MNI152NLin6Asym:res-2 \
--cifti-output 91k \
--random-seed 12345 \
--skull-strip-fixed-seed \
--skull-strip-t1w force \
--notrack \
--md-only-boilerplate \
--skip-bids-validation \
--stop-on-first-crash \
--fs-license-file /SGLR/FREESURFER_HOME/license.txt \
--nprocs 2 \
--omp-nthreads 2 \
--mem-mb 16000 \
--participant-label "${subid}"
```

produces (ds005747 sub-011, fMRIPrep 25.2.5)

```
sub-011_desc-aparcaseg_dseg.nii.gz
sub-011_desc-aseg_dseg.nii.gz
sub-011_desc-brain_mask.json
sub-011_desc-brain_mask.nii.gz
sub-011_desc-preproc_T1w.json
sub-011_desc-preproc_T1w.nii.gz
sub-011_desc-ribbon_mask.json
sub-011_desc-ribbon_mask.nii.gz
sub-011_dseg.nii.gz
sub-011_from-fsnative_to-T1w_mode-image_xfm.txt
sub-011_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5
sub-011_from-MNI152NLin6Asym_to-T1w_mode-image_xfm.h5
sub-011_from-T1w_to-fsnative_mode-image_xfm.txt
sub-011_from-T1w_to-MNI152NLin2009cAsym_mode-image_xfm.h5
sub-011_from-T1w_to-MNI152NLin6Asym_mode-image_xfm.h5
sub-011_hemi-L_curv.shape.gii
sub-011_hemi-L_desc-cortex_mask.json
sub-011_hemi-L_desc-cortex_mask.label.gii
sub-011_hemi-L_inflated.surf.gii
sub-011_hemi-L_midthickness.surf.gii
sub-011_hemi-L_pial.surf.gii
sub-011_hemi-L_space-fsaverage_desc-reg_sphere.surf.gii
sub-011_hemi-L_space-fsLR_den-32k_midthickness.surf.gii
sub-011_hemi-L_space-fsLR_den-32k_pial.surf.gii
sub-011_hemi-L_space-fsLR_den-32k_white.surf.gii
sub-011_hemi-L_space-fsLR_desc-msmsulc_sphere.surf.gii
sub-011_hemi-L_space-fsLR_desc-reg_sphere.surf.gii
sub-011_hemi-L_sphere.surf.gii
sub-011_hemi-L_sulc.shape.gii
sub-011_hemi-L_thickness.shape.gii
sub-011_hemi-L_white.surf.gii
sub-011_hemi-R_curv.shape.gii
sub-011_hemi-R_desc-cortex_mask.json
sub-011_hemi-R_desc-cortex_mask.label.gii
sub-011_hemi-R_inflated.surf.gii
sub-011_hemi-R_midthickness.surf.gii
sub-011_hemi-R_pial.surf.gii
sub-011_hemi-R_space-fsaverage_desc-reg_sphere.surf.gii
sub-011_hemi-R_space-fsLR_den-32k_midthickness.surf.gii
sub-011_hemi-R_space-fsLR_den-32k_pial.surf.gii
sub-011_hemi-R_space-fsLR_den-32k_white.surf.gii
sub-011_hemi-R_space-fsLR_desc-msmsulc_sphere.surf.gii
sub-011_hemi-R_space-fsLR_desc-reg_sphere.surf.gii
sub-011_hemi-R_sphere.surf.gii
sub-011_hemi-R_sulc.shape.gii
sub-011_hemi-R_thickness.shape.gii
sub-011_hemi-R_white.surf.gii
sub-011_label-CSF_probseg.nii.gz
sub-011_label-GM_probseg.nii.gz
sub-011_label-WM_probseg.nii.gz
sub-011_space-fsLR_den-91k_curv.dscalar.nii
sub-011_space-fsLR_den-91k_curv.json
sub-011_space-fsLR_den-91k_sulc.dscalar.nii
sub-011_space-fsLR_den-91k_sulc.json
sub-011_space-fsLR_den-91k_thickness.dscalar.nii
sub-011_space-fsLR_den-91k_thickness.json
sub-011_space-MNI152NLin2009cAsym_res-2_desc-brain_mask.json
sub-011_space-MNI152NLin2009cAsym_res-2_desc-brain_mask.nii.gz
sub-011_space-MNI152NLin2009cAsym_res-2_desc-preproc_T1w.json
sub-011_space-MNI152NLin2009cAsym_res-2_desc-preproc_T1w.nii.gz
sub-011_space-MNI152NLin2009cAsym_res-2_dseg.json
sub-011_space-MNI152NLin2009cAsym_res-2_dseg.nii.gz
sub-011_space-MNI152NLin2009cAsym_res-2_label-CSF_probseg.nii.gz
sub-011_space-MNI152NLin2009cAsym_res-2_label-GM_probseg.nii.gz
sub-011_space-MNI152NLin2009cAsym_res-2_label-WM_probseg.nii.gz
sub-011_space-MNI152NLin6Asym_res-2_desc-brain_mask.json
sub-011_space-MNI152NLin6Asym_res-2_desc-brain_mask.nii.gz
sub-011_space-MNI152NLin6Asym_res-2_desc-preproc_T1w.json
sub-011_space-MNI152NLin6Asym_res-2_desc-preproc_T1w.nii.gz
sub-011_space-MNI152NLin6Asym_res-2_dseg.json
sub-011_space-MNI152NLin6Asym_res-2_dseg.nii.gz
sub-011_space-MNI152NLin6Asym_res-2_label-CSF_probseg.nii.gz
sub-011_space-MNI152NLin6Asym_res-2_label-GM_probseg.nii.gz
sub-011_space-MNI152NLin6Asym_res-2_label-WM_probseg.nii.gz
```

## `minimal`

```bash
singularity run \
-B "${PWD}" \
--containall \
--pwd "${PWD}" \
-B $JOB_TMP:/tmp \
-B /templateflow:/templateflow \
-B /license.txt:/SGLR/FREESURFER_HOME/license.txt \
--env TEMPLATEFLOW_HOME=/templateflow \
"containers/.datalad/environments/bids-fmriprep/image" \
"${PWD}/sourcedata/raw" \
"${PWD}/outputs/fMRIPrep-25.2.5+minimal" \
participant \
-w .git/tmp/wkdir \
--level minimal \
--output-spaces MNI152NLin2009cAsym:res-2 MNI152NLin6Asym:res-2 \
--cifti-output 91k \
--random-seed 12345 \
--skull-strip-fixed-seed \
--skull-strip-t1w force \
--use-syn-sdc warn \
--me-output-echos \
--notrack \
--md-only-boilerplate \
--skip-bids-validation \
--stop-on-first-crash \
--fs-license-file /SGLR/FREESURFER_HOME/license.txt \
--fs-subjects-dir "${PWD}"/sourcedata/fMRIPrep-25.2.5+anat/fMRIPrep-25.2.5+anat/sourcedata/freesurfer \
--nprocs 4 \
--omp-nthreads 2 \
--mem-mb 32000 \
--participant-label "${subid}"
```

produces (ds005747 sub-011, 3 BOLD runs)

```
sub-011_task-rest_run-01_desc-brain_mask.json
sub-011_task-rest_run-01_desc-brain_mask.nii.gz
sub-011_task-rest_run-01_desc-coreg_boldref.json
sub-011_task-rest_run-01_desc-coreg_boldref.nii.gz
sub-011_task-rest_run-01_desc-hmc_boldref.json
sub-011_task-rest_run-01_desc-hmc_boldref.nii.gz
sub-011_task-rest_run-01_from-boldref_to-auto00000_mode-image_desc-fmap_xfm.json
sub-011_task-rest_run-01_from-boldref_to-auto00000_mode-image_desc-fmap_xfm.txt
sub-011_task-rest_run-01_from-boldref_to-T1w_mode-image_desc-coreg_xfm.json
sub-011_task-rest_run-01_from-boldref_to-T1w_mode-image_desc-coreg_xfm.txt
sub-011_task-rest_run-01_from-orig_to-boldref_mode-image_desc-hmc_xfm.json
sub-011_task-rest_run-01_from-orig_to-boldref_mode-image_desc-hmc_xfm.txt
sub-011_task-rest_run-02_desc-brain_mask.json
sub-011_task-rest_run-02_desc-brain_mask.nii.gz
sub-011_task-rest_run-02_desc-coreg_boldref.json
sub-011_task-rest_run-02_desc-coreg_boldref.nii.gz
sub-011_task-rest_run-02_desc-hmc_boldref.json
sub-011_task-rest_run-02_desc-hmc_boldref.nii.gz
sub-011_task-rest_run-02_from-boldref_to-auto00001_mode-image_desc-fmap_xfm.json
sub-011_task-rest_run-02_from-boldref_to-auto00001_mode-image_desc-fmap_xfm.txt
sub-011_task-rest_run-02_from-boldref_to-T1w_mode-image_desc-coreg_xfm.json
sub-011_task-rest_run-02_from-boldref_to-T1w_mode-image_desc-coreg_xfm.txt
sub-011_task-rest_run-02_from-orig_to-boldref_mode-image_desc-hmc_xfm.json
sub-011_task-rest_run-02_from-orig_to-boldref_mode-image_desc-hmc_xfm.txt
sub-011_task-rest_run-03_desc-brain_mask.json
sub-011_task-rest_run-03_desc-brain_mask.nii.gz
sub-011_task-rest_run-03_desc-coreg_boldref.json
sub-011_task-rest_run-03_desc-coreg_boldref.nii.gz
sub-011_task-rest_run-03_desc-hmc_boldref.json
sub-011_task-rest_run-03_desc-hmc_boldref.nii.gz
sub-011_task-rest_run-03_from-boldref_to-auto00002_mode-image_desc-fmap_xfm.json
sub-011_task-rest_run-03_from-boldref_to-auto00002_mode-image_desc-fmap_xfm.txt
sub-011_task-rest_run-03_from-boldref_to-T1w_mode-image_desc-coreg_xfm.json
sub-011_task-rest_run-03_from-boldref_to-T1w_mode-image_desc-coreg_xfm.txt
sub-011_task-rest_run-03_from-orig_to-boldref_mode-image_desc-hmc_xfm.json
sub-011_task-rest_run-03_from-orig_to-boldref_mode-image_desc-hmc_xfm.txt
```

If additional output spaces are needed, please comment here. If they only show up on a full run, it may relate to our plans to compute-on-the-fly to generate files that are cheap to create but expensive to store.

Contributor guide

No contributing guide indexed for this repository

Research direction

Review the `anat` and `minimal` command examples and their listed outputs for dataset ds005747, subject `sub-011`. The issue asks for feedback about additional output spaces, but does not identify a code entry point or a specific change; completion would require an agreed output-space requirement before implementation can be defined.

Written by the indexing model from the issue text.

Assessment

Tech stack
python, shell
Domain
data
Issue type
Feature
Difficulty
5/5
Estimated time
Over a week
Activity status
Active
Clarity
Needs clarification
Newbie friendliness
25/100

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