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CI: Add test data (#100)
* CI: Add test data * ENH: Add BCP run to circle tests * CI: Add jobs to workflow, tidy up nibabies call * DOCKER: Cache MNIInfant cohort-1 * CI: Add sudo to apt-get calls * CI: Update data cache * CI: Fix bcp data cache * TST: Update data path, run anatomical first * CI: Add git config values * FIX: Ensure ca certificates are installed and uptodate * MAINT: Ensure derivatives are also fetched * MAINT: Use miniconda to install datalad/git-annex * TST: Avoid using gin hosted subdataset * FIX: Update derivatives paths * TST: Avoid datalad symlinks * CI: Simplify download code if data exists, bump bcp cache * CI: Add coreutils for missing cp flags * CI: Remove lingering fi * CI: Add outputs file to verify anatomical results * CI: Clean up output checking code, add full nibabies run * CI: Switch to tree for dir traversal * CI: Finalize full run outputs * CI: Remove working directory artifacts, ensure full derivatives are saved instead
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‎.circleci/bcp_anat_outputs.txt‎

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.bidsignore
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dataset_description.json
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desc-aparcaseg_dseg.tsv
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desc-aseg_dseg.tsv
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logs
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logs/CITATION.bib
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logs/CITATION.md
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logs/CITATION.tex
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sub-01
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sub-01.html
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sub-01/ses-1mo
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sub-01/ses-1mo/anat
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-1_desc-aparcaseg_dseg.nii.gz
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-1_desc-aseg_dseg.nii.gz
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-1_desc-brain_mask.json
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-1_desc-brain_mask.nii.gz
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-1_desc-preproc_T1w.json
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-1_desc-preproc_T1w.nii.gz
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-1_dseg.nii.gz
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-1_from-fsnative_to-T1w_mode-image_xfm.txt
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-1_from-MNIInfant+1_to-T1w_mode-image_xfm.h5
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-1_from-T1w_to-fsnative_mode-image_xfm.txt
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-1_from-T1w_to-MNIInfant+1_mode-image_xfm.h5
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-1_hemi-L_inflated.surf.gii
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-1_hemi-L_midthickness.surf.gii
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-1_hemi-L_pial.surf.gii
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-1_hemi-L_smoothwm.surf.gii
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-1_hemi-R_inflated.surf.gii
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-1_hemi-R_midthickness.surf.gii
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-1_hemi-R_pial.surf.gii
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-1_hemi-R_smoothwm.surf.gii
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-1_label-CSF_probseg.nii.gz
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-1_label-GM_probseg.nii.gz
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-1_label-WM_probseg.nii.gz
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-1_space-MNIInfant_cohort-1_desc-brain_mask.json
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-1_space-MNIInfant_cohort-1_desc-brain_mask.nii.gz
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-1_space-MNIInfant_cohort-1_desc-preproc_T1w.json
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-1_space-MNIInfant_cohort-1_desc-preproc_T1w.nii.gz
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-1_space-MNIInfant_cohort-1_dseg.nii.gz
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-1_space-MNIInfant_cohort-1_label-CSF_probseg.nii.gz
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-1_space-MNIInfant_cohort-1_label-GM_probseg.nii.gz
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-1_space-MNIInfant_cohort-1_label-WM_probseg.nii.gz

‎.circleci/bcp_full_outputs.txt‎

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dataset_description.json
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desc-aparcaseg_dseg.tsv
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desc-aseg_dseg.tsv
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logs
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logs/CITATION.bib
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logs/CITATION.md
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logs/CITATION.tex
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sub-01
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sub-01.html
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sub-01/ses-1mo
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sub-01/ses-1mo/anat
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-1_desc-aparcaseg_dseg.nii.gz
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-1_desc-aseg_dseg.nii.gz
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-1_desc-brain_mask.json
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-1_desc-brain_mask.nii.gz
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-1_desc-preproc_T1w.json
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-1_desc-preproc_T1w.nii.gz
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-1_dseg.nii.gz
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-1_from-fsnative_to-T1w_mode-image_xfm.txt
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-1_from-MNIInfant+1_to-T1w_mode-image_xfm.h5
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-1_from-T1w_to-fsnative_mode-image_xfm.txt
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-1_from-T1w_to-MNIInfant+1_mode-image_xfm.h5
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-1_hemi-L_inflated.surf.gii
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-1_hemi-L_midthickness.surf.gii
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-1_hemi-L_pial.surf.gii
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-1_hemi-L_smoothwm.surf.gii
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-1_hemi-R_inflated.surf.gii
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-1_hemi-R_midthickness.surf.gii
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-1_hemi-R_pial.surf.gii
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-1_hemi-R_smoothwm.surf.gii
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-1_label-CSF_probseg.nii.gz
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-1_label-GM_probseg.nii.gz
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-1_label-WM_probseg.nii.gz
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-1_space-MNIInfant_cohort-1_desc-brain_mask.json
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-1_space-MNIInfant_cohort-1_desc-brain_mask.nii.gz
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-1_space-MNIInfant_cohort-1_desc-preproc_T1w.json
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-1_space-MNIInfant_cohort-1_desc-preproc_T1w.nii.gz
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-1_space-MNIInfant_cohort-1_dseg.nii.gz
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-1_space-MNIInfant_cohort-1_label-CSF_probseg.nii.gz
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-1_space-MNIInfant_cohort-1_label-GM_probseg.nii.gz
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-1_space-MNIInfant_cohort-1_label-WM_probseg.nii.gz
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sub-01/ses-1mo/fmap
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sub-01/ses-1mo/fmap/sub-01_ses-1mo_run-1_fmapid-auto00000_desc-coeff_fieldmap.nii.gz
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sub-01/ses-1mo/fmap/sub-01_ses-1mo_run-1_fmapid-auto00000_desc-epi_fieldmap.nii.gz
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sub-01/ses-1mo/fmap/sub-01_ses-1mo_run-1_fmapid-auto00000_desc-preproc_fieldmap.json
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sub-01/ses-1mo/fmap/sub-01_ses-1mo_run-1_fmapid-auto00000_desc-preproc_fieldmap.nii.gz
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sub-01/ses-1mo/func
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sub-01/ses-1mo/func/sub-01_ses-1mo_task-rest_acq-PA_run-1_boldref.nii.gz
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sub-01/ses-1mo/func/sub-01_ses-1mo_task-rest_acq-PA_run-1_desc-brain_mask.json
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sub-01/ses-1mo/func/sub-01_ses-1mo_task-rest_acq-PA_run-1_desc-brain_mask.nii.gz
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sub-01/ses-1mo/func/sub-01_ses-1mo_task-rest_acq-PA_run-1_desc-confounds_timeseries.json
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sub-01/ses-1mo/func/sub-01_ses-1mo_task-rest_acq-PA_run-1_desc-confounds_timeseries.tsv
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sub-01/ses-1mo/func/sub-01_ses-1mo_task-rest_acq-PA_run-1_desc-preproc_bold.json
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sub-01/ses-1mo/func/sub-01_ses-1mo_task-rest_acq-PA_run-1_desc-preproc_bold.nii.gz
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sub-01/ses-1mo/func/sub-01_ses-1mo_task-rest_acq-PA_run-1_from-scanner_to-T1w_mode-image_xfm.txt
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sub-01/ses-1mo/func/sub-01_ses-1mo_task-rest_acq-PA_run-1_from-T1w_to-scanner_mode-image_xfm.txt
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sub-01/ses-1mo/func/sub-01_ses-1mo_task-rest_acq-PA_run-1_space-MNIInfant_cohort-1_boldref.nii.gz
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sub-01/ses-1mo/func/sub-01_ses-1mo_task-rest_acq-PA_run-1_space-MNIInfant_cohort-1_desc-aparcaseg_dseg.nii.gz
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sub-01/ses-1mo/func/sub-01_ses-1mo_task-rest_acq-PA_run-1_space-MNIInfant_cohort-1_desc-aseg_dseg.nii.gz
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sub-01/ses-1mo/func/sub-01_ses-1mo_task-rest_acq-PA_run-1_space-MNIInfant_cohort-1_desc-brain_mask.json
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sub-01/ses-1mo/func/sub-01_ses-1mo_task-rest_acq-PA_run-1_space-MNIInfant_cohort-1_desc-brain_mask.nii.gz
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sub-01/ses-1mo/func/sub-01_ses-1mo_task-rest_acq-PA_run-1_space-MNIInfant_cohort-1_desc-preproc_bold.json
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sub-01/ses-1mo/func/sub-01_ses-1mo_task-rest_acq-PA_run-1_space-MNIInfant_cohort-1_desc-preproc_bold.nii.gz

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