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Merge pull request #2036 from oesteban/enh/1175-smriprep-fasttrack
ENH: Side-track *sMRIPrep* if a path of anatomical derivatives is given
2 parents a0cc490 + 3edced6 commit 9509b31

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‎.circleci/config.yml‎

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‎.circleci/ds005_fasttrack_outputs.txt‎

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fmriprep
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fmriprep/dataset_description.json
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fmriprep/desc-aparcaseg_dseg.tsv
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fmriprep/desc-aseg_dseg.tsv
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fmriprep/logs
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fmriprep/logs/CITATION.bib
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fmriprep/logs/CITATION.html
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fmriprep/logs/CITATION.md
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fmriprep/logs/CITATION.tex
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fmriprep/sub-01
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fmriprep/sub-01/func
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_AROMAnoiseICs.csv
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-confounds_regressors.json
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-confounds_regressors.tsv
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-MELODIC_mixing.tsv
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-fsaverage5_hemi-L.func.gii
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-fsaverage5_hemi-R.func.gii
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-fsLR_den-91k_bold.dtseries.json
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-fsLR_den-91k_bold.dtseries.nii
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-fsnative_hemi-L.func.gii
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-fsnative_hemi-R.func.gii
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-MNI152NLin2009cAsym_boldref.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-MNI152NLin2009cAsym_desc-aparcaseg_dseg.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-MNI152NLin2009cAsym_desc-aseg_dseg.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-MNI152NLin2009cAsym_desc-brain_mask.json
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-MNI152NLin2009cAsym_desc-preproc_bold.json
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-MNI152NLin6Asym_boldref.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-MNI152NLin6Asym_desc-aparcaseg_dseg.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-MNI152NLin6Asym_desc-aseg_dseg.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-MNI152NLin6Asym_desc-brain_mask.json
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-MNI152NLin6Asym_desc-brain_mask.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-MNI152NLin6Asym_desc-preproc_bold.json
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-MNI152NLin6Asym_desc-preproc_bold.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-MNI152NLin6Asym_desc-smoothAROMAnonaggr_bold.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-T1w_boldref.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-T1w_desc-aparcaseg_dseg.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-T1w_desc-aseg_dseg.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-T1w_desc-brain_mask.json
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-T1w_desc-brain_mask.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-T1w_desc-preproc_bold.json
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-T1w_desc-preproc_bold.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_AROMAnoiseICs.csv
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-confounds_regressors.json
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-confounds_regressors.tsv
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-MELODIC_mixing.tsv
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-fsaverage5_hemi-L.func.gii
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-fsaverage5_hemi-R.func.gii
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-fsLR_den-91k_bold.dtseries.json
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-fsLR_den-91k_bold.dtseries.nii
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-fsnative_hemi-L.func.gii
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-fsnative_hemi-R.func.gii
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin2009cAsym_boldref.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin2009cAsym_desc-aparcaseg_dseg.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin2009cAsym_desc-aseg_dseg.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin2009cAsym_desc-brain_mask.json
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin2009cAsym_desc-preproc_bold.json
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin6Asym_boldref.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin6Asym_desc-aparcaseg_dseg.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin6Asym_desc-aseg_dseg.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin6Asym_desc-brain_mask.json
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin6Asym_desc-brain_mask.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin6Asym_desc-preproc_bold.json
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin6Asym_desc-preproc_bold.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin6Asym_desc-smoothAROMAnonaggr_bold.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-T1w_boldref.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-T1w_desc-aparcaseg_dseg.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-T1w_desc-aseg_dseg.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-T1w_desc-brain_mask.json
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-T1w_desc-brain_mask.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-T1w_desc-preproc_bold.json
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-T1w_desc-preproc_bold.nii.gz
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fmriprep/sub-01.html
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/tmp/ds005/derivatives

‎.circleci/ds005_partial_fasttrack_outputs.txt‎

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fmriprep
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fmriprep/dataset_description.json
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fmriprep/desc-aparcaseg_dseg.tsv
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fmriprep/desc-aseg_dseg.tsv
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fmriprep/logs
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fmriprep/logs/CITATION.bib
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fmriprep/logs/CITATION.html
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fmriprep/logs/CITATION.md
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fmriprep/logs/CITATION.tex
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fmriprep/sub-01
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fmriprep/sub-01/func
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_AROMAnoiseICs.csv
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-confounds_regressors.json
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-confounds_regressors.tsv
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-MELODIC_mixing.tsv
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-fsaverage5_hemi-L.func.gii
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-fsaverage5_hemi-R.func.gii
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-fsLR_den-91k_bold.dtseries.json
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-fsLR_den-91k_bold.dtseries.nii
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-fsnative_hemi-L.func.gii
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-fsnative_hemi-R.func.gii
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin2009cAsym_boldref.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin2009cAsym_desc-aparcaseg_dseg.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin2009cAsym_desc-aseg_dseg.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin2009cAsym_desc-brain_mask.json
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin2009cAsym_desc-preproc_bold.json
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin6Asym_boldref.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin6Asym_desc-aparcaseg_dseg.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin6Asym_desc-aseg_dseg.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin6Asym_desc-brain_mask.json
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin6Asym_desc-brain_mask.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin6Asym_desc-preproc_bold.json
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin6Asym_desc-preproc_bold.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin6Asym_desc-smoothAROMAnonaggr_bold.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-T1w_boldref.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-T1w_desc-aparcaseg_dseg.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-T1w_desc-aseg_dseg.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-T1w_desc-brain_mask.json
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-T1w_desc-brain_mask.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-T1w_desc-preproc_bold.json
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-T1w_desc-preproc_bold.nii.gz
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fmriprep/sub-01.html
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/tmp/ds005/derivatives_partial

‎.circleci/ds054_fasttrack_outputs.txt‎

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fmriprep/dataset_description.json
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fmriprep/logs
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fmriprep/logs/CITATION.bib
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fmriprep/logs/CITATION.html
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fmriprep/logs/CITATION.md
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fmriprep/logs/CITATION.tex
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fmriprep/sub-100185
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fmriprep/sub-100185/func
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fmriprep/sub-100185/func/sub-100185_task-machinegame_run-01_boldref.nii.gz
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fmriprep/sub-100185/func/sub-100185_task-machinegame_run-01_desc-brain_mask.json
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fmriprep/sub-100185/func/sub-100185_task-machinegame_run-01_desc-brain_mask.nii.gz
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fmriprep/sub-100185/func/sub-100185_task-machinegame_run-01_desc-confounds_regressors.json
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fmriprep/sub-100185/func/sub-100185_task-machinegame_run-01_desc-confounds_regressors.tsv
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fmriprep/sub-100185/func/sub-100185_task-machinegame_run-01_desc-preproc_bold.json
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fmriprep/sub-100185/func/sub-100185_task-machinegame_run-01_desc-preproc_bold.nii.gz
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fmriprep/sub-100185/func/sub-100185_task-machinegame_run-01_space-MNI152NLin2009cAsym_res-2_boldref.nii.gz
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fmriprep/sub-100185/func/sub-100185_task-machinegame_run-01_space-MNI152NLin2009cAsym_res-2_desc-brain_mask.json
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fmriprep/sub-100185/func/sub-100185_task-machinegame_run-01_space-MNI152NLin2009cAsym_res-2_desc-brain_mask.nii.gz
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fmriprep/sub-100185/func/sub-100185_task-machinegame_run-01_space-MNI152NLin2009cAsym_res-2_desc-preproc_bold.json
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fmriprep/sub-100185/func/sub-100185_task-machinegame_run-01_space-T1w_boldref.nii.gz
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fmriprep/sub-100185/func/sub-100185_task-machinegame_run-01_space-T1w_desc-brain_mask.json
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fmriprep/sub-100185/func/sub-100185_task-machinegame_run-01_space-T1w_desc-brain_mask.nii.gz
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fmriprep/sub-100185/func/sub-100185_task-machinegame_run-01_space-T1w_desc-preproc_bold.json
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fmriprep/sub-100185/func/sub-100185_task-machinegame_run-01_space-T1w_desc-preproc_bold.nii.gz
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fmriprep/sub-100185/func/sub-100185_task-machinegame_run-02_boldref.nii.gz
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fmriprep/sub-100185/func/sub-100185_task-machinegame_run-02_desc-brain_mask.json
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fmriprep/sub-100185/func/sub-100185_task-machinegame_run-02_desc-brain_mask.nii.gz
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fmriprep/sub-100185/func/sub-100185_task-machinegame_run-02_desc-confounds_regressors.json
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fmriprep/sub-100185/func/sub-100185_task-machinegame_run-02_desc-confounds_regressors.tsv
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fmriprep/sub-100185/func/sub-100185_task-machinegame_run-02_desc-preproc_bold.json
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fmriprep/sub-100185/func/sub-100185_task-machinegame_run-02_desc-preproc_bold.nii.gz
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fmriprep/sub-100185/func/sub-100185_task-machinegame_run-02_space-MNI152NLin2009cAsym_res-2_boldref.nii.gz
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fmriprep/sub-100185/func/sub-100185_task-machinegame_run-02_space-MNI152NLin2009cAsym_res-2_desc-brain_mask.json
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fmriprep/sub-100185/func/sub-100185_task-machinegame_run-02_space-MNI152NLin2009cAsym_res-2_desc-preproc_bold.json
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fmriprep/sub-100185/func/sub-100185_task-machinegame_run-02_space-T1w_boldref.nii.gz
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fmriprep/sub-100185/func/sub-100185_task-machinegame_run-02_space-T1w_desc-brain_mask.json
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fmriprep/sub-100185/func/sub-100185_task-machinegame_run-02_space-T1w_desc-brain_mask.nii.gz
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fmriprep/sub-100185/func/sub-100185_task-machinegame_run-02_space-T1w_desc-preproc_bold.json
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fmriprep/sub-100185/func/sub-100185_task-machinegame_run-02_space-T1w_desc-preproc_bold.nii.gz
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fmriprep/sub-100185.html
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/tmp/ds054/derivatives

‎.circleci/ds210_fasttrack_outputs.txt‎

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fmriprep/dataset_description.json
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fmriprep/logs
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fmriprep/logs/CITATION.bib
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fmriprep/logs/CITATION.html
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fmriprep/logs/CITATION.md
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fmriprep/logs/CITATION.tex
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fmriprep/sub-02
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fmriprep/sub-02/func
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fmriprep/sub-02/func/sub-02_task-cuedSGT_run-01_desc-confounds_regressors.json
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fmriprep/sub-02/func/sub-02_task-cuedSGT_run-01_desc-confounds_regressors.tsv
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fmriprep/sub-02/func/sub-02_task-cuedSGT_run-01_space-MNI152NLin2009cAsym_boldref.nii.gz
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fmriprep/sub-02/func/sub-02_task-cuedSGT_run-01_space-MNI152NLin2009cAsym_desc-brain_mask.json
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fmriprep/sub-02/func/sub-02_task-cuedSGT_run-01_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz
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fmriprep/sub-02/func/sub-02_task-cuedSGT_run-01_space-MNI152NLin2009cAsym_desc-preproc_bold.json
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fmriprep/sub-02/func/sub-02_task-cuedSGT_run-01_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz
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fmriprep/sub-02.html
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/tmp/ds210/derivatives

‎docs/faq.rst‎

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Additionally, consider using the ``--low-mem`` flag, which will make some memory optimizations at the cost of disk space in the working directory.
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I have already run ``recon-all`` on my subjects, can I reuse my outputs?
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------------------------------------------------------------------------
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Yes, as long as the FreeSurfer_ version previously used was ``6.0.0`` or newer.
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If running with FreeSurfer, *fMRIPrep* checks if the output directory contains a ``freesurfer``
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directory and reuses the outputs found.
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Alternatively, you can use the ``--fs-subjects-dir`` flag to specify a different location for the existing FreeSurfer outputs.
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ERROR: it appears that ``recon-all`` is already running
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-------------------------------------------------------
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When running FreeSurfer's ``recon-all``, an error may say *it appears it is already running*.
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As suggested by the ``recon-all`` output message, deleting these files will enable
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FreeSurfer to execute ``recon-all`` again.
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In general, please be cautious of deleting files and mindful why a file may exist.
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Running subjects in parallel
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----------------------------
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When running several subjects in parallel, and depending on your settings, fMRIPrep may
@@ -223,7 +219,6 @@ If you are a Singularity user, please check out :ref:`singularity_tf`.
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How do I select only certain files to be input to fMRIPrep?
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-----------------------------------------------------------
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Using the ``--bids-filter-file`` flag, you can pass fMRIPrep a JSON file that
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describes a custom BIDS filter for selecting files with PyBIDS, with the syntax
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``{<query>: {<entity>: <filter>, ...},...}``. For example::
@@ -271,3 +266,22 @@ Therefore, if your *fMRIPrep* process crashes and you attempt to re-run it reusi
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as much as it could from the previous run, you can either make sure that
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the default ``$PWD/work/`` points to a reasonable, reusable path in your environment or
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configure a better location on your with ``-w <PATH>``.
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Can I use *fMRIPrep* for longitudinal studies?
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----------------------------------------------
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As partially indicated before, *fMRIPrep* assumes no substantial anatomical changes happen
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across sessions.
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When substantial changes are expected, special considerations must be taken.
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Some examples follow:
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* Surgery: use only pre-operation sessions for the anatomical data. This will typically be done
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by omitting post-operation sessions from the inputs to *fMRIPrep*.
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* Developing and elderly populations: there is currently no standard way of processing these.
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However, `as suggested by U. Tooley at NeuroStars.org
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<https://neurostars.org/t/fmriprep-how-to-reuse-longitudinal-and-pre-run-freesurfer/4585/15>`__,
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it is theoretically possible to leverage the *anatomical fast-track* along with the
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``--bids-filters`` option to process sessions fully independently, or grouped by some study-design
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criteria.
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Please check the `link
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<https://neurostars.org/t/fmriprep-how-to-reuse-longitudinal-and-pre-run-freesurfer/4585/15>`__
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for further information on this approach.

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