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MAINT: Merge master into multiecho #1324

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merged 120 commits into from
Oct 26, 2018
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725fa73
[MAINT] Pin grabbit and pybids in ``setup.py``
oesteban Sep 14, 2018
375c7d3
FIX: Enhance T2 contrast in reference estimate
effigies Sep 26, 2018
d8fbf00
TEST: Plot old/new masks
effigies Aug 10, 2018
26e0f44
Merge pull request #1299 from poldracklab/fix/enhance_t2
oesteban Oct 2, 2018
2c2ab47
FIX: Create template from one usable T1w image
effigies Oct 3, 2018
3e55760
STY: Whitespace
effigies Oct 3, 2018
ab36915
Merge pull request #1305 from poldracklab/fix/structural_reference
oesteban Oct 3, 2018
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
3a20826
CI: Deploy poldracklab/fmriprep:unstable tracking master
effigies 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
6f74072
Merge pull request #1284 from poldracklab/oesteban-patch-1
oesteban Oct 4, 2018
165df97
Version 1.1.8 - Update CHANGES [skip ci]
oesteban Oct 4, 2018
d617210
Merge pull request #1306 from oesteban/enh/issue-960
oesteban Oct 5, 2018
3befabb
[skip ci] Add YAML file with list of subject that were included in th…
oesteban Oct 5, 2018
2ee473e
[skip ci] Add quotes to string
oesteban Oct 5, 2018
4384681
clean-up caches
oesteban Oct 6, 2018
c19a51a
fix BIDS-validator link
surchs Oct 9, 2018
ec5e651
[ENH] Template-based masking of EPI boldrefs
oesteban Oct 15, 2018
3e344db
fix flake8 error
oesteban Oct 15, 2018
2679533
use poldracklab/niworkflows@0946bad69867840718d4aeeb54ef11bd535c1a9c
oesteban Oct 15, 2018
af0cd52
update pinning to release
oesteban Oct 15, 2018
b5aa8bd
update reports.py
alioco Oct 15, 2018
c088fb6
new registration parameters
oesteban Oct 16, 2018
966d412
pre-cache template getter
oesteban Oct 16, 2018
be17090
fix ds005 problem
oesteban Oct 16, 2018
e121073
Merge pull request #1320 from surchs/master
effigies Oct 16, 2018
76d0f70
1) shorten registration; 2) accept a ``pre_mask``
oesteban Oct 16, 2018
713132f
[skip ci] update documentation
oesteban Oct 16, 2018
0c9e665
CI: Update expected anatomical outputs
effigies Oct 17, 2018
bc502a1
RF: Update anatomical derivatives for RC1
effigies Oct 17, 2018
9f6ca76
[HOTFIX] Missing BOLD reports
oesteban Oct 17, 2018
8bb0241
Merge pull request #1326 from poldracklab/hotfix/reports-2
oesteban Oct 17, 2018
18fe6ca
Merge remote-tracking branch 'upstream/master' into fix/1000
oesteban Oct 17, 2018
eca0cf8
Merge remote-tracking branch 'upstream/master' into bids/derivatives_rc1
oesteban Oct 17, 2018
ba58d8d
fix problems in derivatives datasink
oesteban Oct 17, 2018
9ef8ee1
[HOTFIX] Reportlets - bbregister vs flirtbbr (continues #1326)
oesteban Oct 17, 2018
4dc0908
Merge branch 'hotfix/reports-3' into fix/1000
oesteban Oct 17, 2018
fbe25f0
Merge pull request #1322 from alioco/master
oesteban Oct 17, 2018
450ac3a
Merge branch 'hotfix/reports-3' into bids/derivatives_rc1
oesteban Oct 17, 2018
96f97d6
fix mandatory suffix
oesteban Oct 17, 2018
5da2e92
disambiguate flirt reportlets
oesteban Oct 17, 2018
30d7658
Merge branch 'hotfix/reports-3' into fix/1000
oesteban Oct 17, 2018
3c6303d
Merge pull request #1328 from poldracklab/hotfix/reports-3
oesteban Oct 17, 2018
46411d3
Merge remote-tracking branch 'upstream/master' into bids/derivatives_rc1
oesteban Oct 17, 2018
aa0841b
``_roi`` -> ``_dseg`` (incl. functionals)
oesteban Oct 17, 2018
6215779
[TST] Add heavily-nonuniform boldrefs for regression tests
oesteban Oct 17, 2018
48fdaa0
do not build docs on ``test/`` branches
oesteban Oct 17, 2018
8a974fb
make cache key consistent
oesteban Oct 17, 2018
f36e2eb
is restoring cache necessary in the job?
oesteban Oct 18, 2018
b814d61
CI: Tar up directory for OSF publication
effigies Oct 16, 2018
b6021c4
FIX: Set inputs in inputs object
effigies Oct 16, 2018
da18127
CI: Add -svx options to pytest
effigies Oct 16, 2018
edaa53b
fix problems
oesteban Oct 17, 2018
c1bea4a
fix tarring new masks
oesteban Oct 17, 2018
20325c6
pacify flake8
oesteban Oct 17, 2018
9f69ba7
minor fixes to test
oesteban Oct 18, 2018
ecb1185
clear regression tests cache
oesteban Oct 18, 2018
36b369e
[skip ci] pacify flake8
oesteban Oct 18, 2018
53a96a8
Merge pull request #1329 from poldracklab/tests/add-more-masks
oesteban Oct 18, 2018
65e6fbc
Merge remote-tracking branch 'upstream/master' into fix/1000
oesteban Oct 18, 2018
9b67991
[FIX] Quick update to new template structure
oesteban Oct 18, 2018
fb7806e
Merge remote-tracking branch 'upstream/master' into bids/derivatives_rc1
oesteban Oct 18, 2018
ee574ff
Merge branch 'fix/osf-templates' into bids/derivatives_rc1
oesteban Oct 18, 2018
acb8584
fix ds054 whitelist of outputs
oesteban Oct 18, 2018
2fffaed
[skip ds210][skip tests][skip docs] Clear ds005 cache
oesteban Oct 18, 2018
9f768f4
Merge pull request #1330 from oesteban/fix/osf-templates
oesteban Oct 18, 2018
235aa1c
[skip tests][skip docs][skip ds210][skip ds054] pass mask into ica-ar…
jdkent Oct 18, 2018
cbcf075
[skip ci] Fix ordering of ds054 outputs whitelist
oesteban Oct 18, 2018
c9bfe4f
Merge pull request #1325 from effigies/bids/derivatives_rc1
oesteban Oct 18, 2018
c6a7405
[skip ds005][skip tests][skip docs] Clear caches
oesteban Oct 19, 2018
cdf1f9d
[skip ci] Merge remote-tracking branch 'upstream/master' into add_aro…
oesteban Oct 19, 2018
4caeb9c
Merge pull request #1332 from jdkent/add_aroma_mask
oesteban Oct 19, 2018
b3f34a5
[skip tests][skip docs][skip ds210][skip ds054] wip: remove non stead…
jdkent Oct 20, 2018
b4ab300
[skip tests][skip docs][skip ds210][skip ds054] pacify flake8
jdkent Oct 20, 2018
921bf56
[skip ds210][skip ds054] update the documentation
jdkent Oct 21, 2018
d773cfc
[skip tests][skip docs][skip ds210][skip ds054][skip ds005]
jdkent Oct 21, 2018
c05b7bb
Merge pull request #1336 from jdkent/patch-1
effigies Oct 21, 2018
99f9a23
Merge branch 'master' of https://github.com/poldracklab/fmriprep into…
jdkent Oct 21, 2018
b9e5ff4
remove whitespace
jdkent Oct 23, 2018
11ea1c2
[skip ds210][skip ds054][skip tests] switch n_volumes* to skip_vols a…
jdkent Oct 23, 2018
fabc7c9
[skip tests][skip ds210][skip ds054][skip ds005] add --bind method to…
jdkent Oct 23, 2018
05f445f
CI: Update functional outputs
effigies Oct 17, 2018
117fe8a
Functional derivatives
effigies Oct 17, 2018
266ba15
fix unused variable as excuse to trigger tests
oesteban Oct 19, 2018
11b3e44
Merge pull request #1340 from jdkent/singularity_docs
effigies Oct 23, 2018
a296a79
Merge pull request #1307 from effigies/docker/unstable
effigies Oct 23, 2018
7a512c3
FIX: AROMA/CIFTI names
effigies Oct 23, 2018
51a1021
STY: Unused variable [skip ds005][skip ds054][skip ds210]
effigies Oct 23, 2018
a0460f9
Merge pull request #1333 from effigies/bids/derivatives_rc1
oesteban Oct 24, 2018
8ba55fa
Merge remote-tracking branch 'upstream/master' into fix/1000
oesteban Oct 24, 2018
0448135
Fix to set mod
kasbohm Oct 24, 2018
949b504
[skip ds210][skip ds054][skip tests][skip docs] edits from effigies r…
jdkent Oct 24, 2018
698e821
fix header mismatch problem
oesteban Oct 24, 2018
e52394e
[skip ci] Pin niworkflows==0.4.4
oesteban Oct 24, 2018
2a09ae8
address @effigies' comments on MatchHeader
oesteban Oct 24, 2018
a44b9b4
re-order parameters in docstrings [skip ds210][skip ds054][skip ds005]
jdkent Oct 24, 2018
f86b543
fix master
oesteban Oct 24, 2018
9503750
Merge branch 'ds005/expected-outputs' into fix/1000
oesteban Oct 25, 2018
ca32147
remove one branch
oesteban Oct 25, 2018
736d5d9
fix ordering of expected outputs
oesteban Oct 25, 2018
7535a08
[skip ci] fix minimal error in docs
oesteban Oct 25, 2018
874c4ce
Merge pull request #1321 from oesteban/fix/1000
oesteban Oct 25, 2018
e706408
Merge pull request #1344 from oesteban/ds005/expected-outputs
oesteban Oct 25, 2018
b71ddf3
ENH: Deprecate --debug with --sloppy
effigies Oct 25, 2018
6922e8d
[TST] Add doctest for #1339
oesteban Oct 25, 2018
8eaf472
DOC: Update order, grouping of options [skip ds005][skip ds054][skip …
effigies Oct 25, 2018
666b306
CI: Run sloppy registration
effigies Oct 25, 2018
4141206
Merge pull request #1 from oesteban/test/doctest-1339
kasbohm Oct 25, 2018
3de9874
Added name
kasbohm Oct 25, 2018
0d582f6
Merge pull request #1346 from kasbohm/patch-1
oesteban Oct 25, 2018
b71a9d3
Merge pull request #1347 from effigies/fix/debug_flags
effigies Oct 25, 2018
8f73452
[skip ci] Update notebooks
oesteban Oct 25, 2018
053aa16
Merge remote-tracking branch 'upstream/multiecho' into sync/master_mu…
emdupre Oct 26, 2018
aa56aaa
Merge pull request #1335 from jdkent/remove_init_vol_aroma
effigies Oct 26, 2018
c542dbf
Merge remote-tracking branch 'upstream/master' into sync/master_multi…
effigies Oct 26, 2018
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112 changes: 58 additions & 54 deletions .circleci/ds005_outputs.txt
Original file line number Diff line number Diff line change
@@ -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_boldref.nii.gz
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_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_boldref.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_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_boldref.nii.gz
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_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_boldref.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_label-aparcaseg_roi.nii.gz
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fmriprep/sub-01.html
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fmriprep/logs/CITATION.tex
fmriprep/sub-01
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fmriprep/sub-01.html
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fmriprep/logs/CITATION.tex
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fmriprep/sub-100185.html
/tmp/ds054/derivatives
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