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[ENH] Store BOLD reference images #1306

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merged 7 commits into from
Oct 5, 2018
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[ENH] Store BOLD reference images #1306

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b718242
update circle outputs
oesteban Oct 4, 2018
b8c897f
first steps in #960. Includes modifications pertaining to #1302
oesteban Oct 4, 2018
15f48fd
actually generate references
oesteban Oct 4, 2018
887cd3e
fix import path
oesteban Oct 4, 2018
b867453
fix ds210
oesteban Oct 4, 2018
9f2e25d
use _boldref suffix. close #960
oesteban Oct 4, 2018
1da1419
fix ordering of derivatives
oesteban Oct 4, 2018
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112 changes: 58 additions & 54 deletions .circleci/ds005_outputs.txt
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Expand Up @@ -6,60 +6,64 @@ fmriprep/logs/CITATION.md
fmriprep/logs/CITATION.tex
fmriprep/sub-01
fmriprep/sub-01/anat
fmriprep/sub-01/anat/sub-01_T1w_brainmask.nii.gz
fmriprep/sub-01/anat/sub-01_T1w_class-CSF_probtissue.nii.gz
fmriprep/sub-01/anat/sub-01_T1w_class-GM_probtissue.nii.gz
fmriprep/sub-01/anat/sub-01_T1w_class-WM_probtissue.nii.gz
fmriprep/sub-01/anat/sub-01_T1w_dtissue.nii.gz
fmriprep/sub-01/anat/sub-01_T1w_inflated.L.surf.gii
fmriprep/sub-01/anat/sub-01_T1w_inflated.R.surf.gii
fmriprep/sub-01/anat/sub-01_T1w_label-aparcaseg_roi.nii.gz
fmriprep/sub-01/anat/sub-01_T1w_label-aseg_roi.nii.gz
fmriprep/sub-01/anat/sub-01_T1w_midthickness.L.surf.gii
fmriprep/sub-01/anat/sub-01_T1w_midthickness.R.surf.gii
fmriprep/sub-01/anat/sub-01_T1w_pial.L.surf.gii
fmriprep/sub-01/anat/sub-01_T1w_pial.R.surf.gii
fmriprep/sub-01/anat/sub-01_T1w_preproc.nii.gz
fmriprep/sub-01/anat/sub-01_T1w_smoothwm.L.surf.gii
fmriprep/sub-01/anat/sub-01_T1w_smoothwm.R.surf.gii
fmriprep/sub-01/anat/sub-01_T1w_space-MNI152NLin2009cAsym_brainmask.nii.gz
fmriprep/sub-01/anat/sub-01_T1w_space-MNI152NLin2009cAsym_class-CSF_probtissue.nii.gz
fmriprep/sub-01/anat/sub-01_T1w_space-MNI152NLin2009cAsym_class-GM_probtissue.nii.gz
fmriprep/sub-01/anat/sub-01_T1w_space-MNI152NLin2009cAsym_class-WM_probtissue.nii.gz
fmriprep/sub-01/anat/sub-01_T1w_space-MNI152NLin2009cAsym_dtissue.nii.gz
fmriprep/sub-01/anat/sub-01_T1w_space-MNI152NLin2009cAsym_preproc.nii.gz
fmriprep/sub-01/anat/sub-01_T1w_space-MNI152NLin2009cAsym_target-T1w_warp.h5
fmriprep/sub-01/anat/sub-01_T1w_space-orig_target-T1w_affine.txt
fmriprep/sub-01/anat/sub-01_T1w_target-fsnative_affine.txt
fmriprep/sub-01/anat/sub-01_T1w_target-MNI152NLin2009cAsym_warp.h5
fmriprep/sub-01/anat/sub-01_brainmask.nii.gz
fmriprep/sub-01/anat/sub-01_class-CSF_probtissue.nii.gz
fmriprep/sub-01/anat/sub-01_class-GM_probtissue.nii.gz
fmriprep/sub-01/anat/sub-01_class-WM_probtissue.nii.gz
fmriprep/sub-01/anat/sub-01_dtissue.nii.gz
fmriprep/sub-01/anat/sub-01_inflated.L.surf.gii
fmriprep/sub-01/anat/sub-01_inflated.R.surf.gii
fmriprep/sub-01/anat/sub-01_label-aparcaseg_roi.nii.gz
fmriprep/sub-01/anat/sub-01_label-aseg_roi.nii.gz
fmriprep/sub-01/anat/sub-01_midthickness.L.surf.gii
fmriprep/sub-01/anat/sub-01_midthickness.R.surf.gii
fmriprep/sub-01/anat/sub-01_pial.L.surf.gii
fmriprep/sub-01/anat/sub-01_pial.R.surf.gii
fmriprep/sub-01/anat/sub-01_preproc.nii.gz
fmriprep/sub-01/anat/sub-01_smoothwm.L.surf.gii
fmriprep/sub-01/anat/sub-01_smoothwm.R.surf.gii
fmriprep/sub-01/anat/sub-01_space-MNI152NLin2009cAsym_brainmask.nii.gz
fmriprep/sub-01/anat/sub-01_space-MNI152NLin2009cAsym_class-CSF_probtissue.nii.gz
fmriprep/sub-01/anat/sub-01_space-MNI152NLin2009cAsym_class-GM_probtissue.nii.gz
fmriprep/sub-01/anat/sub-01_space-MNI152NLin2009cAsym_class-WM_probtissue.nii.gz
fmriprep/sub-01/anat/sub-01_space-MNI152NLin2009cAsym_dtissue.nii.gz
fmriprep/sub-01/anat/sub-01_space-MNI152NLin2009cAsym_preproc.nii.gz
fmriprep/sub-01/anat/sub-01_space-MNI152NLin2009cAsym_target-T1w_warp.h5
fmriprep/sub-01/anat/sub-01_space-orig_target-T1w_affine.txt
fmriprep/sub-01/anat/sub-01_target-fsnative_affine.txt
fmriprep/sub-01/anat/sub-01_target-MNI152NLin2009cAsym_warp.h5
fmriprep/sub-01/func
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_bold_AROMAnoiseICs.csv
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_bold_confounds.tsv
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_bold_MELODICmix.tsv
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_bold_space-cifti_variant-space1_preproc.dtseries.json
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_bold_space-cifti_variant-space1_preproc.dtseries.nii
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_bold_space-fsaverage5.L.func.gii
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_bold_space-fsaverage5.R.func.gii
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_bold_space-MNI152NLin2009cAsym_brainmask.nii.gz
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_bold_space-MNI152NLin2009cAsym_preproc.nii.gz
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_bold_space-MNI152NLin2009cAsym_variant-smoothAROMAnonaggr_preproc.nii.gz
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_bold_space-T1w_brainmask.nii.gz
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_bold_space-T1w_label-aparcaseg_roi.nii.gz
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_bold_space-T1w_label-aseg_roi.nii.gz
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_bold_space-T1w_preproc.nii.gz
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_bold_AROMAnoiseICs.csv
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_bold_confounds.tsv
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_bold_MELODICmix.tsv
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_bold_space-cifti_variant-space1_preproc.dtseries.json
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_bold_space-cifti_variant-space1_preproc.dtseries.nii
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_bold_space-fsaverage5.L.func.gii
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_bold_space-fsaverage5.R.func.gii
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_bold_space-MNI152NLin2009cAsym_brainmask.nii.gz
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_bold_space-MNI152NLin2009cAsym_preproc.nii.gz
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_bold_space-MNI152NLin2009cAsym_variant-smoothAROMAnonaggr_preproc.nii.gz
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_bold_space-T1w_brainmask.nii.gz
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_bold_space-T1w_label-aparcaseg_roi.nii.gz
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_bold_space-T1w_label-aseg_roi.nii.gz
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_bold_space-T1w_preproc.nii.gz
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_AROMAnoiseICs.csv
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_confounds.tsv
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_MELODICmix.tsv
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-cifti_variant-space1_preproc.dtseries.json
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-cifti_variant-space1_preproc.dtseries.nii
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-fsaverage5.L.func.gii
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-fsaverage5.R.func.gii
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-MNI152NLin2009cAsym_brainmask.nii.gz
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-MNI152NLin2009cAsym_desc-3dref_bold.nii.gz
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I don't think this qualifies as a bold.nii.gz, as it's not a 4D time series. We didn't try to get a ref suffix (or perhaps boldref, since there is no longer a bold entry) into RC1, but we can still use it as long as there isn't a more appropriate suffix in the spec.

Pinging BIDS-meister @chrisfilo for a second opinion, though.

fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-MNI152NLin2009cAsym_preproc.nii.gz
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-MNI152NLin2009cAsym_variant-smoothAROMAnonaggr_preproc.nii.gz
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-T1w_brainmask.nii.gz
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-T1w_desc-3dref_bold.nii.gz
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-T1w_label-aparcaseg_roi.nii.gz
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-T1w_label-aseg_roi.nii.gz
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-T1w_preproc.nii.gz
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_AROMAnoiseICs.csv
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_confounds.tsv
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_MELODICmix.tsv
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-cifti_variant-space1_preproc.dtseries.json
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-cifti_variant-space1_preproc.dtseries.nii
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-fsaverage5.L.func.gii
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-fsaverage5.R.func.gii
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin2009cAsym_brainmask.nii.gz
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin2009cAsym_desc-3dref_bold.nii.gz
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin2009cAsym_preproc.nii.gz
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin2009cAsym_variant-smoothAROMAnonaggr_preproc.nii.gz
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-T1w_brainmask.nii.gz
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-T1w_desc-3dref_bold.nii.gz
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-T1w_label-aparcaseg_roi.nii.gz
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-T1w_label-aseg_roi.nii.gz
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-T1w_preproc.nii.gz
fmriprep/sub-01.html
/tmp/ds005/derivatives
82 changes: 42 additions & 40 deletions .circleci/ds005_partial_outputs.txt
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Expand Up @@ -6,46 +6,48 @@ fmriprep/logs/CITATION.md
fmriprep/logs/CITATION.tex
fmriprep/sub-01
fmriprep/sub-01/anat
fmriprep/sub-01/anat/sub-01_T1w_brainmask.nii.gz
fmriprep/sub-01/anat/sub-01_T1w_class-CSF_probtissue.nii.gz
fmriprep/sub-01/anat/sub-01_T1w_class-GM_probtissue.nii.gz
fmriprep/sub-01/anat/sub-01_T1w_class-WM_probtissue.nii.gz
fmriprep/sub-01/anat/sub-01_T1w_dtissue.nii.gz
fmriprep/sub-01/anat/sub-01_T1w_inflated.L.surf.gii
fmriprep/sub-01/anat/sub-01_T1w_inflated.R.surf.gii
fmriprep/sub-01/anat/sub-01_T1w_label-aparcaseg_roi.nii.gz
fmriprep/sub-01/anat/sub-01_T1w_label-aseg_roi.nii.gz
fmriprep/sub-01/anat/sub-01_T1w_midthickness.L.surf.gii
fmriprep/sub-01/anat/sub-01_T1w_midthickness.R.surf.gii
fmriprep/sub-01/anat/sub-01_T1w_pial.L.surf.gii
fmriprep/sub-01/anat/sub-01_T1w_pial.R.surf.gii
fmriprep/sub-01/anat/sub-01_T1w_preproc.nii.gz
fmriprep/sub-01/anat/sub-01_T1w_smoothwm.L.surf.gii
fmriprep/sub-01/anat/sub-01_T1w_smoothwm.R.surf.gii
fmriprep/sub-01/anat/sub-01_T1w_space-MNI152NLin2009cAsym_brainmask.nii.gz
fmriprep/sub-01/anat/sub-01_T1w_space-MNI152NLin2009cAsym_class-CSF_probtissue.nii.gz
fmriprep/sub-01/anat/sub-01_T1w_space-MNI152NLin2009cAsym_class-GM_probtissue.nii.gz
fmriprep/sub-01/anat/sub-01_T1w_space-MNI152NLin2009cAsym_class-WM_probtissue.nii.gz
fmriprep/sub-01/anat/sub-01_T1w_space-MNI152NLin2009cAsym_dtissue.nii.gz
fmriprep/sub-01/anat/sub-01_T1w_space-MNI152NLin2009cAsym_preproc.nii.gz
fmriprep/sub-01/anat/sub-01_T1w_space-MNI152NLin2009cAsym_target-T1w_warp.h5
fmriprep/sub-01/anat/sub-01_T1w_space-orig_target-T1w_affine.txt
fmriprep/sub-01/anat/sub-01_T1w_target-fsnative_affine.txt
fmriprep/sub-01/anat/sub-01_T1w_target-MNI152NLin2009cAsym_warp.h5
fmriprep/sub-01/anat/sub-01_brainmask.nii.gz
fmriprep/sub-01/anat/sub-01_class-CSF_probtissue.nii.gz
fmriprep/sub-01/anat/sub-01_class-GM_probtissue.nii.gz
fmriprep/sub-01/anat/sub-01_class-WM_probtissue.nii.gz
fmriprep/sub-01/anat/sub-01_dtissue.nii.gz
fmriprep/sub-01/anat/sub-01_inflated.L.surf.gii
fmriprep/sub-01/anat/sub-01_inflated.R.surf.gii
fmriprep/sub-01/anat/sub-01_label-aparcaseg_roi.nii.gz
fmriprep/sub-01/anat/sub-01_label-aseg_roi.nii.gz
fmriprep/sub-01/anat/sub-01_midthickness.L.surf.gii
fmriprep/sub-01/anat/sub-01_midthickness.R.surf.gii
fmriprep/sub-01/anat/sub-01_pial.L.surf.gii
fmriprep/sub-01/anat/sub-01_pial.R.surf.gii
fmriprep/sub-01/anat/sub-01_preproc.nii.gz
fmriprep/sub-01/anat/sub-01_smoothwm.L.surf.gii
fmriprep/sub-01/anat/sub-01_smoothwm.R.surf.gii
fmriprep/sub-01/anat/sub-01_space-MNI152NLin2009cAsym_brainmask.nii.gz
fmriprep/sub-01/anat/sub-01_space-MNI152NLin2009cAsym_class-CSF_probtissue.nii.gz
fmriprep/sub-01/anat/sub-01_space-MNI152NLin2009cAsym_class-GM_probtissue.nii.gz
fmriprep/sub-01/anat/sub-01_space-MNI152NLin2009cAsym_class-WM_probtissue.nii.gz
fmriprep/sub-01/anat/sub-01_space-MNI152NLin2009cAsym_dtissue.nii.gz
fmriprep/sub-01/anat/sub-01_space-MNI152NLin2009cAsym_preproc.nii.gz
fmriprep/sub-01/anat/sub-01_space-MNI152NLin2009cAsym_target-T1w_warp.h5
fmriprep/sub-01/anat/sub-01_space-orig_target-T1w_affine.txt
fmriprep/sub-01/anat/sub-01_target-fsnative_affine.txt
fmriprep/sub-01/anat/sub-01_target-MNI152NLin2009cAsym_warp.h5
fmriprep/sub-01/func
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_bold_AROMAnoiseICs.csv
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_bold_confounds.tsv
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_bold_MELODICmix.tsv
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_bold_space-cifti_variant-space1_preproc.dtseries.json
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_bold_space-cifti_variant-space1_preproc.dtseries.nii
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_bold_space-fsaverage5.L.func.gii
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_bold_space-fsaverage5.R.func.gii
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_bold_space-MNI152NLin2009cAsym_preproc.nii.gz
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_bold_space-MNI152NLin2009cAsym_variant-smoothAROMAnonaggr_preproc.nii.gz
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_bold_space-T1w_brainmask.nii.gz
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_bold_space-T1w_label-aparcaseg_roi.nii.gz
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_bold_space-T1w_label-aseg_roi.nii.gz
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_bold_space-T1w_preproc.nii.gz
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_AROMAnoiseICs.csv
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_confounds.tsv
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_MELODICmix.tsv
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-cifti_variant-space1_preproc.dtseries.json
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-cifti_variant-space1_preproc.dtseries.nii
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-fsaverage5.L.func.gii
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-fsaverage5.R.func.gii
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-MNI152NLin2009cAsym_brainmask.nii.gz
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-MNI152NLin2009cAsym_desc-3dref_bold.nii.gz
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-MNI152NLin2009cAsym_preproc.nii.gz
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-MNI152NLin2009cAsym_variant-smoothAROMAnonaggr_preproc.nii.gz
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-T1w_brainmask.nii.gz
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-T1w_desc-3dref_bold.nii.gz
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-T1w_label-aparcaseg_roi.nii.gz
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-T1w_label-aseg_roi.nii.gz
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-T1w_preproc.nii.gz
fmriprep/sub-01.html
/tmp/ds005/derivatives_partial
54 changes: 29 additions & 25 deletions .circleci/ds054_outputs.txt
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fmriprep/logs/CITATION.tex
fmriprep/sub-100185
fmriprep/sub-100185/anat
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fmriprep/sub-100185/func
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fmriprep/sub-100185/func/sub-100185_task-machinegame_run-01_bold_space-T1w_brainmask.nii.gz
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fmriprep/sub-100185/func/sub-100185_task-machinegame_run-02_bold_space-MNI152NLin2009cAsym_brainmask.nii.gz
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fmriprep/sub-100185/func/sub-100185_task-machinegame_run-01_confounds.tsv
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fmriprep/sub-100185/func/sub-100185_task-machinegame_run-01_space-T1w_brainmask.nii.gz
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fmriprep/sub-100185/func/sub-100185_task-machinegame_run-02_space-MNI152NLin2009cAsym_preproc.nii.gz
fmriprep/sub-100185/func/sub-100185_task-machinegame_run-02_space-T1w_brainmask.nii.gz
fmriprep/sub-100185/func/sub-100185_task-machinegame_run-02_space-T1w_desc-3dref_bold.nii.gz
fmriprep/sub-100185/func/sub-100185_task-machinegame_run-02_space-T1w_preproc.nii.gz
fmriprep/sub-100185.html
/tmp/ds054/derivatives