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‎.circleci/config.yml

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‎.circleci/ds005_outputs.txt

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fmriprep/sub-01/anat/sub-01_T1w_space-orig_target-T1w_affine.txt
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fmriprep/sub-01/anat/sub-01_T1w_target-fsnative_affine.txt
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fmriprep/sub-01/anat/sub-01_T1w_target-MNI152NLin2009cAsym_warp.h5
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fmriprep/sub-01/figures
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fmriprep/sub-01/figures/sub-01_T1w_reconall.svg
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fmriprep/sub-01/figures/sub-01_T1w_seg_brainmask.svg
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fmriprep/sub-01/figures/sub-01_T1w_t1_2_mni.svg
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fmriprep/sub-01/figures/sub-01_task-mixedgamblestask_run-01_bold_bbr.svg
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fmriprep/sub-01/figures/sub-01_task-mixedgamblestask_run-01_bold_ica_aroma.svg
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fmriprep/sub-01/figures/sub-01_task-mixedgamblestask_run-01_bold_rois.svg
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fmriprep/sub-01/figures/sub-01_task-mixedgamblestask_run-01_bold_sdc_syn.svg
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fmriprep/sub-01/figures/sub-01_task-mixedgamblestask_run-02_bold_bbr.svg
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fmriprep/sub-01/figures/sub-01_task-mixedgamblestask_run-02_bold_ica_aroma.svg
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fmriprep/sub-01/figures/sub-01_task-mixedgamblestask_run-02_bold_rois.svg
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fmriprep/sub-01/figures/sub-01_task-mixedgamblestask_run-02_bold_sdc_syn.svg
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fmriprep/sub-01/func
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_bold_AROMAnoiseICs.csv
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_bold_confounds.tsv
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_bold_MELODICmix.tsv
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_bold_space-cifti_variant-space1_preproc.dtseries.json
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_bold_space-cifti_variant-space1_preproc.dtseries.nii
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_bold_space-fsaverage5.L.func.gii
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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_brainmask.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_bold_AROMAnoiseICs.csv
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_bold_confounds.tsv
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_bold_MELODICmix.tsv
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_bold_space-cifti_variant-space1_preproc.dtseries.json
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_bold_space-cifti_variant-space1_preproc.dtseries.nii
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_bold_space-fsaverage5.L.func.gii
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_bold_space-fsaverage5.R.func.gii
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_bold_space-MNI152NLin2009cAsym_brainmask.nii.gz

‎.circleci/ds005_partial_outputs.txt

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fmriprep
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fmriprep/logs
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fmriprep/sub-01
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fmriprep/sub-01/anat
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fmriprep/sub-01/anat/sub-01_T1w_brainmask.nii.gz
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fmriprep/sub-01/anat/sub-01_T1w_class-CSF_probtissue.nii.gz
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fmriprep/sub-01/anat/sub-01_T1w_class-GM_probtissue.nii.gz
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fmriprep/sub-01/anat/sub-01_T1w_class-WM_probtissue.nii.gz
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fmriprep/sub-01/anat/sub-01_T1w_dtissue.nii.gz
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fmriprep/sub-01/anat/sub-01_T1w_inflated.L.surf.gii
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fmriprep/sub-01/anat/sub-01_T1w_inflated.R.surf.gii
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fmriprep/sub-01/anat/sub-01_T1w_label-aparcaseg_roi.nii.gz
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fmriprep/sub-01/anat/sub-01_T1w_label-aseg_roi.nii.gz
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fmriprep/sub-01/anat/sub-01_T1w_midthickness.L.surf.gii
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fmriprep/sub-01/anat/sub-01_T1w_midthickness.R.surf.gii
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fmriprep/sub-01/anat/sub-01_T1w_pial.L.surf.gii
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fmriprep/sub-01/anat/sub-01_T1w_pial.R.surf.gii
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fmriprep/sub-01/anat/sub-01_T1w_preproc.nii.gz
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fmriprep/sub-01/anat/sub-01_T1w_smoothwm.L.surf.gii
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fmriprep/sub-01/anat/sub-01_T1w_smoothwm.R.surf.gii
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fmriprep/sub-01/anat/sub-01_T1w_space-MNI152NLin2009cAsym_brainmask.nii.gz
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fmriprep/sub-01/anat/sub-01_T1w_space-MNI152NLin2009cAsym_class-CSF_probtissue.nii.gz
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fmriprep/sub-01/anat/sub-01_T1w_space-MNI152NLin2009cAsym_class-GM_probtissue.nii.gz
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fmriprep/sub-01/anat/sub-01_T1w_space-MNI152NLin2009cAsym_class-WM_probtissue.nii.gz
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fmriprep/sub-01/anat/sub-01_T1w_space-MNI152NLin2009cAsym_dtissue.nii.gz
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fmriprep/sub-01/anat/sub-01_T1w_space-MNI152NLin2009cAsym_preproc.nii.gz
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fmriprep/sub-01/anat/sub-01_T1w_space-MNI152NLin2009cAsym_target-T1w_warp.h5
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fmriprep/sub-01/anat/sub-01_T1w_space-orig_target-T1w_affine.txt
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fmriprep/sub-01/anat/sub-01_T1w_target-fsnative_affine.txt
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fmriprep/sub-01/anat/sub-01_T1w_target-MNI152NLin2009cAsym_warp.h5
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fmriprep/sub-01/func
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_bold_AROMAnoiseICs.csv
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_bold_confounds.tsv
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_bold_MELODICmix.tsv
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_bold_space-cifti_variant-space1_preproc.dtseries.json
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_bold_space-cifti_variant-space1_preproc.dtseries.nii
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_bold_space-fsaverage5.L.func.gii
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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_brainmask.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_bold_space-MNI152NLin2009cAsym_preproc.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_bold_space-MNI152NLin2009cAsym_variant-smoothAROMAnonaggr_preproc.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_bold_space-T1w_brainmask.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_bold_space-T1w_label-aparcaseg_roi.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_bold_space-T1w_label-aseg_roi.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_bold_space-T1w_preproc.nii.gz
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fmriprep/sub-01.html
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/tmp/ds005/derivatives_partial

‎.circleci/ds054_outputs.txt

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fmriprep/sub-100185/anat/sub-100185_T1w_space-orig_target-T1w_affine.txt
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fmriprep/sub-100185/anat/sub-100185_T1w_target-MNI152NLin2009cAsym_warp.h5
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fmriprep/sub-100185/figures
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fmriprep/sub-100185/figures/sub-100185_phasediff_fmap_mask.svg
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fmriprep/sub-100185/figures/sub-100185_T1w_seg_brainmask.svg
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fmriprep/sub-100185/figures/sub-100185_T1w_t1_2_mni.svg
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fmriprep/sub-100185/figures/sub-100185_task-machinegame_run-01_bold_flt_bbr.svg
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fmriprep/sub-100185/figures/sub-100185_task-machinegame_run-01_bold_fmap_reg.svg
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fmriprep/sub-100185/figures/sub-100185_task-machinegame_run-01_bold_fmap_reg_vsm.svg
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fmriprep/sub-100185/figures/sub-100185_task-machinegame_run-01_bold_forcedsyn.svg
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fmriprep/sub-100185/figures/sub-100185_task-machinegame_run-01_bold_rois.svg
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fmriprep/sub-100185/figures/sub-100185_task-machinegame_run-01_bold_sdc_phasediff.svg
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fmriprep/sub-100185/figures/sub-100185_task-machinegame_run-02_bold_flt_bbr.svg
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fmriprep/sub-100185/figures/sub-100185_task-machinegame_run-02_bold_fmap_reg.svg
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fmriprep/sub-100185/figures/sub-100185_task-machinegame_run-02_bold_fmap_reg_vsm.svg
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fmriprep/sub-100185/figures/sub-100185_task-machinegame_run-02_bold_forcedsyn.svg
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fmriprep/sub-100185/figures/sub-100185_task-machinegame_run-02_bold_rois.svg
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fmriprep/sub-100185/figures/sub-100185_task-machinegame_run-02_bold_sdc_phasediff.svg
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fmriprep/sub-100185/func/sub-100185_task-machinegame_run-01_bold_space-MNI152NLin2009cAsym_brainmask.nii.gz

‎.circleci/ds000210_outputs.txt renamed to ‎.circleci/ds210_outputs.txt

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fmriprep/sub-02/anat/sub-02_T1w_space-orig_target-T1w_affine.txt
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fmriprep/sub-02/figures/sub-02_T1w_t1_2_mni.svg
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fmriprep/sub-02/figures/sub-02_task-cuedSGT_run-01_echo-1_bold_flirt.svg
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fmriprep/sub-02/figures/sub-02_task-cuedSGT_run-01_echo-1_bold_rois.svg
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fmriprep/sub-02/figures/sub-02_task-cuedSGT_run-01_echo-1_bold_sdc_syn.svg
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/tmp/ds210/derivatives

‎.gitmodules

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[submodule "notebooks"]
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path = notebooks
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url = https://github.com/poldracklab/fmriprep-notebooks.git

‎.zenodo.json

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"affiliation": "Speech & Hearing Bioscience & Technology Program, Harvard University",
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"orcid": "0000-0002-2172-5786"
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},
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{
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"name": "Gomez, Daniel E. P.",
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"affiliation": "Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen",
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"orcid": "0000-0001-8635-021X"
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},
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{
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"name": "Lurie, Daniel J.",
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"affiliation": "Department of Psychology, University of California, Berkeley",
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"orcid": "0000-0001-8012-6399"
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},
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{
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"name": "Ye, Zhifang",
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"affiliation": "State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University",
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"orcid": "0000-0003-0489-2619"
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},
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"affiliation": "Department of Psychology, Stanford University",

‎CHANGES.rst

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1.1.2 (July 6, 2018)
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====================
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This release incorporates Nipype improvements that should reduce the
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chance of hanging if tasks are killed for excessive resource consumption.
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Thanks to Elizabeth DuPre for documentation updates.
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* [DOC] Clarify how to reuse FreeSurfer derivatives (#1189)
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* [DOC] Improve command line option documentation (#1186, #1080)
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* [MAINT] Update core dependencies (#1179, #1180)
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1.1.1 (June 7, 2018)
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====================
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* [ENH] Pre-cache DKT31 template in Docker image (#1159)
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* [MAINT] Update core dependencies (#1163)
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1.1.0 (June 4, 2018)
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====================
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* [ENH] Use Reorient interface included upstream in nipype (#1153)
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* [FIX] Refine BIDS queries to avoid indexing derivatives (#1141)
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* [DOC] Clarify outlier columns (#1138)
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* [PIN] Update to niworkflows 0.4.0 and nipype 1.0.4 (#1133)
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1.0.15 (May 17, 2018)
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=====================
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* [DOC] Add lesion masking during registration (#1113)
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* [FIX] Patch ``boldbuffer`` for ME (#1134)
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1.0.14 (May 15, 2018)
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=====================
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With thanks to @ZhifangYe for contributions
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* [FIX] Non-invertible transforms bringing parcellation to BOLD (#1130)
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* [FIX] Bad connection for ``--medial-surface-nan`` option (#1128)
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1.0.13 (May 11, 2018)
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=====================
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With thanks to @danlurie for the outstanding contribution of #1106
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* [ENH] Some nit picks on reports (#1123)
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* [ENH] Carpetplot + confounds plot (#1114)
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* [ENH] Add constrained cost-function masking to T1-MNI registration (#1106)
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* [FIX] Circular dependency (#1104)
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* [ENH] Set ``PYTHONNOUSERSITE`` in containers (#1103)
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1.0.12 (May 03, 2018)
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=====================
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* [MAINT] fmriprep-docker: Ensure data/output/work paths are absolute (#1089)
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* [ENH] Add usage tracking and centralized error reporting (#1088)
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* [FIX] Ensure one motion IC index is loaded as list (#1096)
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* [TST] Refactoring CircleCI setup (#1098)
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* [FIX] Compression in DataSinks (#1095)
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* [MAINT] fmriprep-docker: Support Python 2/3 without future or other helpers (#1082)
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* [MAINT] Update npm to 10.x (#1087)
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* [DOC] Prefer pre-print over Zenodo doi in boilerplate (#1086)
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* [DOC] Stylistic fix (\`'template'\`) (#1083)
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* [FIX] Run ICA-AROMA in ``MNI152Lin`` 2mm resampling grid (91x109x91 vox) (#1064)
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* [MAINT] Remove cwebp to revert to png (#1081)
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* [ENH] Allow changing the dimensionality of Melodic for AROMA. (#1052)
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* [FIX] Derivatives datasink handling of compression (#1077)
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* [FIX] Check for invalid sform matrices (#1072)
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* [FIX] Check exit code from subprocess (#1073)
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* [DOC] Add preprint fig. 1 to About (#1070)
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* [FIX] Always strip session from T1w for derivative naming (#1071)
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* [DOC] Add RRIDs in the citation boilerplate (#1061)
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* [ENH] Generate CIFTI derivatives (#1001)
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1.0.11 (April 16, 2018)
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=======================
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* [FIX] Do not detrend CSF/WhiteMatter/GlobalSignal (#1058)
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1.0.10 (April 16, 2018)
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=======================
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* [TST] Re-run ds005 with only one BOLD run (#1048)
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* [FIX] Patch subject_summary in reports (#1047)
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1.0.9 (April 10, 2018)
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======================
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With thanks to @danlurie for contributions.
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* [FIX] Connect inputnode to SDC for pepolar images (#1046)
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* [FIX] Pass ``ref_file`` to STC check (#1038)
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* [DOC] Add BBR fallback to user docs. (#1036)
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* [ENH] Revise resampling grid for template outputs (#1040)
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* [MAINT] DataSinks within their workflows (#1021)
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* [ENH] Add FLAIR pial refinement support (#829)
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* [MAINT] Upgrade to pybids 0.5 (#1027)
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* [MAINT] Refactor fieldmap heuristics (#1017)
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* [FIX] Use metadata to select shortest echo as ref_file (#1018)
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* [ENH] Adopt versioneer to compose version names (#1007)
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* [ENH] Handle first echo separately for ME-EPI (#891)
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1.0.8 (February 22, 2018)
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=========================
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‎CONTRIBUTING.md

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# Contributing to FMRIPREP
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# Contributing to fMRIPrep
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Welcome to the FMRIPREP repository! We're excited you're here and want to contribute.
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Welcome to the fMRIPrep repository! We're excited you're here and want to contribute.
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## Practical guide to submitting your contribution
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These guidelines are designed to make it as easy as possible to get involved. If you have any questions that aren't discussed below, please let us know by opening an [issue][link_issues]!
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**1. Comment on an existing issue or open a new issue referencing your addition.**
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This allows other members of the FMRIPREP development team to confirm that you aren't overlapping with work that's currently underway and that everyone is on the same page with the goal of the work you're going to carry out.
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This allows other members of the FMRIPREP development team to confirm that you aren't
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overlapping with work that's currently underway and that everyone is on the same page
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with the goal of the work you're going to carry out.
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[This blog][link_pushpullblog] is a nice explanation of why putting this work in up front is so useful to everyone involved.
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‎Dockerfile

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# Installing WEBP tools
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curl -sSL "https://github.com/maartenmennes/ICA-AROMA/archive/v0.4.4-beta.tar.gz" \
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| tar -xzC /opt/ICA-AROMA --strip-components 1 && \
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chmod +x /opt/ICA-AROMA/ICA_AROMA.py
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ENV PATH=/opt/ICA-AROMA:$PATH
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# Installing and setting up miniconda
104-
RUN curl -sSLO https://repo.continuum.io/miniconda/Miniconda3-4.3.11-Linux-x86_64.sh && \
105-
bash Miniconda3-4.3.11-Linux-x86_64.sh -b -p /usr/local/miniconda && \
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rm Miniconda3-4.3.11-Linux-x86_64.sh
99+
RUN curl -sSLO https://repo.continuum.io/miniconda/Miniconda3-4.5.4-Linux-x86_64.sh && \
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bash Miniconda3-4.5.4-Linux-x86_64.sh -b -p /usr/local/miniconda && \
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rm Miniconda3-4.5.4-Linux-x86_64.sh
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ENV PATH=/usr/local/miniconda/bin:$PATH \
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LANG=C.UTF-8 \
110-
LC_ALL=C.UTF-8
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LC_ALL=C.UTF-8 \
106+
PYTHONNOUSERSITE=1
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# Installing precomputed python packages
113-
RUN conda install -y mkl=2017.0.1 mkl-service; sync &&\
114-
conda install -y numpy=1.12.0 \
115-
scipy=0.18.1 \
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scikit-learn=0.18.1 \
117-
matplotlib=2.0.0 \
118-
pandas=0.19.2 \
109+
RUN conda install -y mkl=2018.0.3 mkl-service; sync &&\
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conda install -y numpy=1.14.3 \
111+
scipy=1.1.0 \
112+
scikit-learn=0.19.1 \
113+
matplotlib=2.2.0 \
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pandas=0.23.0 \
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libxml2=2.9.4 \
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libxslt=1.1.29\
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traits=4.6.0; sync && \
@@ -124,8 +120,9 @@ RUN conda install -y mkl=2017.0.1 mkl-service; sync &&\
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conda clean --all -y; sync && \
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conda clean -tipsy && sync
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127-
# Precaching fonts
128-
RUN python -c "from matplotlib import font_manager"
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# Precaching fonts, set 'Agg' as default backend for matplotlib
124+
RUN python -c "from matplotlib import font_manager" && \
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sed -i 's/\(backend *: \).*$/\1Agg/g' $( python -c "import matplotlib; print(matplotlib.matplotlib_fname())" )
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# Installing Ubuntu packages and cleaning up
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RUN apt-get update && \
@@ -163,9 +160,7 @@ RUN echo "${VERSION}" > /root/src/fmriprep/fmriprep/VERSION && \
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rm -rf ~/.cache/pip
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165162
RUN ldconfig
166-
167-
WORKDIR /root/src/fmriprep
168-
163+
WORKDIR /tmp/
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ENTRYPOINT ["/usr/local/miniconda/bin/fmriprep"]
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ARG BUILD_DATE
@@ -174,8 +169,9 @@ ARG VERSION
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LABEL org.label-schema.build-date=$BUILD_DATE \
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org.label-schema.name="FMRIPREP" \
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org.label-schema.description="FMRIPREP - robust fMRI preprocessing tool" \
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org.label-schema.url="http://fmriprep.readthedocs.io" \
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org.label-schema.url="http://fmriprep.org" \
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org.label-schema.vcs-ref=$VCS_REF \
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org.label-schema.vcs-url="https://github.com/poldracklab/fmriprep" \
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org.label-schema.version=$VERSION \
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org.label-schema.schema-version="1.0"
177+

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