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fmap issue #514

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308d0fe
doc - update doc
Remi-Gau May 29, 2022
8afb872
add badge to readme
Remi-Gau May 29, 2022
6bce06c
change python version for RTD
Remi-Gau May 29, 2022
72c8096
do not fail doc build on warning
Remi-Gau May 29, 2022
94cc7a6
Merge pull request #383 from bids-standard/fix_trans
Remi-Gau May 29, 2022
5e7871e
fix bids report to actually include metadata for functional data
Remi-Gau May 29, 2022
50db7d9
improve reports
Remi-Gau May 30, 2022
c1a2779
Merge pull request #384 from bids-standard/improve_reports
Remi-Gau May 30, 2022
a7a078c
small fix in diagnostic table plotting
Remi-Gau May 30, 2022
8381cf6
fix bug 385 by coercing Nodes and Edges to always be cells
Remi-Gau Jun 3, 2022
0895e91
get_node function return cell is numel(output) > 1 but struct if equa…
Remi-Gau Jun 3, 2022
ab04030
coerce contrasts into cells on loading
Remi-Gau Jun 3, 2022
3dd6d69
add get_edge method
Remi-Gau Jun 3, 2022
c2b9079
add contrast validation method
Remi-Gau Jun 3, 2022
c0722a8
improve get_edge method to handle edges with same source
Remi-Gau Jun 3, 2022
fb7fca3
add get_source_node method
Remi-Gau Jun 3, 2022
dd97f02
ensure written models are valid
Remi-Gau Jun 3, 2022
e07f2db
Merge pull request #386 from Remi-Gau/fix_model
Remi-Gau Jun 3, 2022
1b53a46
fix typo
Remi-Gau Jun 3, 2022
3afc04b
clear variable that would otherwise lead to directly assigning contra…
Remi-Gau Jun 7, 2022
99eac7b
Fix matlab test CI workflow
Remi-Gau Jun 7, 2022
ca2ec87
make sure tests are run in CI when workflow files are changed
Remi-Gau Jun 7, 2022
15d3b6b
improve Description constructor to also accept filenames and not a ju…
Remi-Gau Jun 8, 2022
7294ba1
fix bugs
Remi-Gau Jun 8, 2022
0c0a4a8
allow empty subject directories when going schema less
Remi-Gau Jun 8, 2022
20b9e2a
Merge pull request #388 from bids-standard/desc
Remi-Gau Jun 8, 2022
9f3a94f
fix bids basic transformers row selection
Remi-Gau Jun 10, 2022
e8f6153
fix printing of windows path
Remi-Gau Jun 12, 2022
5bdacb4
fix printing of windows path
Remi-Gau Jun 12, 2022
89da6b5
Merge pull request #389 from Remi-Gau/dev
Remi-Gau Jun 12, 2022
2c88063
Merge pull request #391 from bids-standard/master
Remi-Gau Jun 13, 2022
7b27412
add possibility to skip the manage dependencies step of the layout
Remi-Gau Jun 16, 2022
f603c81
Merge pull request #394 from Remi-Gau/dependencies
Remi-Gau Jun 16, 2022
25b6765
Merge branch 'master' into dev
Remi-Gau Jun 23, 2022
28626a1
fix default stats model when no trial type columns
Remi-Gau Jun 23, 2022
689b1f8
Merge pull request #396 from bids-standard/fix_default_stats_model
Remi-Gau Jun 23, 2022
239e399
allow constant transformer to use char as Values
Remi-Gau Jun 24, 2022
701b761
Merge pull request #397 from bids-standard/improve_constant
Remi-Gau Jun 24, 2022
6126316
improve diagnostic to be able to split by suffix
Remi-Gau Jun 24, 2022
9bf91f5
improve query performance
Remi-Gau Jun 24, 2022
650b32f
return more argument for diagnostic
Remi-Gau Jun 24, 2022
cadc634
Merge pull request #398 from bids-standard/improve_constant
Remi-Gau Jun 24, 2022
c622862
update PR content and title for schema update
Remi-Gau Jun 25, 2022
7106d45
change transformers name to prevent warning madness on Octave because…
Remi-Gau Jun 25, 2022
d8dd823
update miss hit
Remi-Gau Jun 25, 2022
402e17e
Merge pull request #399 from Remi-Gau/update_bot_PR_details
Remi-Gau Jun 25, 2022
1f43499
FCI
Remi-Gau Jun 25, 2022
af2ec78
remove early call to a bids matlab function in test
Remi-Gau Jun 25, 2022
6c0dbb6
remove early call to a bids matlab function in test
Remi-Gau Jun 25, 2022
fbaf622
lint
Remi-Gau Jun 25, 2022
c640907
fix transformers for octave
Remi-Gau Jun 25, 2022
842f004
Merge pull request #400 from Remi-Gau/rename_transformers
Remi-Gau Jun 25, 2022
42b4979
fix order entity octave
Remi-Gau Jun 27, 2022
22073f9
Merge pull request #403 from Remi-Gau/fix_order_entity_octave
Remi-Gau Jun 27, 2022
db8d341
Merge branch 'master' of https://github.com/bids-standard/bids-matlab…
Remi-Gau Jul 1, 2022
0955c45
allow report to deal with unknown suffixes
Remi-Gau Jul 1, 2022
aeb671f
improve replace transformers
Remi-Gau Jul 8, 2022
8df1514
add transformers to label and merge identical rows
Remi-Gau Jul 9, 2022
f565169
update doc
Remi-Gau Jul 9, 2022
986ff44
refactor
Remi-Gau Jul 9, 2022
40ee8d5
add cumulative behavior to label indentical rows
Remi-Gau Jul 9, 2022
06c36d3
refactor
Remi-Gau Jul 9, 2022
915d96f
expand behavior of label rows to support cell type for columns
Remi-Gau Jul 9, 2022
05ae9db
add tests for merge rows
Remi-Gau Jul 9, 2022
d35add1
FCI
Remi-Gau Jul 9, 2022
09242b9
FCI
Remi-Gau Jul 9, 2022
c681278
add inequality to Filter transformer
Remi-Gau Jul 9, 2022
bae2dcf
support regex for Replace transformers
Remi-Gau Jul 10, 2022
b26cc6e
update docs
Remi-Gau Jul 10, 2022
9d6c44c
refactor
Remi-Gau Jul 10, 2022
be54d8e
add possibility to generate json version of transformers
Remi-Gau Jul 10, 2022
f31c37c
add demo transformers split by trials
Remi-Gau Jul 10, 2022
4ab0b05
update help sections
Remi-Gau Jul 10, 2022
1be0891
Merge branch 'master' of https://github.com/bids-standard/bids-matlab…
Remi-Gau Jul 11, 2022
f0f1151
update code to adapt to new schema
Remi-Gau Jul 11, 2022
76566e8
Merge pull request #405 from Remi-Gau/transformers
Remi-Gau Jul 20, 2022
0920ee7
Merge branch 'master' into dev
Remi-Gau Jul 29, 2022
43db3c9
Merge branch 'master' of https://github.com/bids-standard/bids-matlab…
Remi-Gau Jul 29, 2022
41e0369
fix entity order bug
Remi-Gau Jul 29, 2022
9ca332c
return only one datatypes when they are duplicates
Remi-Gau Jul 29, 2022
bee24df
set file modality in constructor
Remi-Gau Jul 30, 2022
f84af1a
Merge pull request #410 from Remi-Gau/dev
Remi-Gau Jul 30, 2022
1b64b9a
get definition will look into metadata if it returns empty in colums
Remi-Gau Jul 30, 2022
4d51f5f
Merge branch 'dev' of https://github.com/bids-standard/bids-matlab in…
Remi-Gau Jul 30, 2022
a9b90af
Merge branch 'master' into dev
Remi-Gau Aug 24, 2022
fb0b0fe
rm old CI
Remi-Gau Aug 24, 2022
bb054e9
remove labels from dependabot config
Remi-Gau Aug 24, 2022
c08206f
fix test that delete schema
Remi-Gau Aug 24, 2022
5d020cd
Merge branch 'master' into dev
Remi-Gau Aug 24, 2022
ac3fe46
Merge branch 'master' into dev
Remi-Gau Aug 29, 2022
876216a
make layout more verbose
Remi-Gau Sep 7, 2022
8aae022
make layout more versbose and make warning mosre useful
Remi-Gau Sep 7, 2022
4fe38b0
only display a . for actually indexed modality
Remi-Gau Sep 8, 2022
127f854
fix octave bug
Remi-Gau Sep 8, 2022
0b11d06
Merge pull request #422 from bids-standard/layout
Remi-Gau Sep 8, 2022
b2b3fd9
Merge branch 'master' into dev
Remi-Gau Sep 9, 2022
d6a31bd
add function to create basic participant.tsv
Remi-Gau Sep 9, 2022
cb102b0
silence warning test for octave
Remi-Gau Sep 9, 2022
5ee025c
Merge pull request #426 from Remi-Gau/participants
Remi-Gau Sep 9, 2022
21a9a9e
make query warning more explicit
Remi-Gau Sep 10, 2022
6fdd553
add extra model validation
Remi-Gau Sep 10, 2022
70c3d28
revert 21a9a9e
Remi-Gau Sep 10, 2022
c450a75
retry more informative error on metadata query
Remi-Gau Sep 10, 2022
bfb599a
remove some old copyrights
Remi-Gau Sep 11, 2022
87e12f3
fix conflicts
Remi-Gau Oct 6, 2022
8187921
lint
Remi-Gau Oct 6, 2022
7bf2f5b
Merge remote-tracking branch 'upstream/master' into dev
Remi-Gau Oct 12, 2022
fc490f5
use new copyright format
Remi-Gau Oct 12, 2022
66913ef
Merge pull request #439 from Remi-Gau/doc
Remi-Gau Oct 12, 2022
255ff04
Merge remote-tracking branch 'upstream/master' into dev
Remi-Gau Oct 17, 2022
53f17e3
update doc
Remi-Gau Oct 21, 2022
8104704
Merge pull request #444 from Remi-Gau/infra
Remi-Gau Oct 21, 2022
af46a92
Merge pull request #378 from bids-standard/demo_File
Remi-Gau Oct 21, 2022
9a97eed
Merge remote-tracking branch 'upstream/master' into dev
Remi-Gau Oct 21, 2022
42805c6
Merge branch 'master' into dev
Remi-Gau Oct 21, 2022
5f0030d
bring back images for contributing
Remi-Gau Oct 21, 2022
45aba5e
fix typo
Remi-Gau Oct 21, 2022
1e95e53
update demos
Remi-Gau Oct 22, 2022
2ef284e
update notebooks and convert to matlab scripts
Remi-Gau Oct 22, 2022
b0b1a83
update notebooks
Remi-Gau Oct 22, 2022
76ba0bd
add test workflow
Remi-Gau Oct 22, 2022
2ba64b4
FCI
Remi-Gau Oct 22, 2022
2d1f964
FCI
Remi-Gau Oct 22, 2022
87b5fdc
fix notebooks
Remi-Gau Oct 22, 2022
35e3f6f
Update demos/working_with_files.m
Remi-Gau Oct 22, 2022
1c6ccb9
update doc
Remi-Gau Oct 22, 2022
579fcec
FCI
Remi-Gau Oct 22, 2022
e584f45
switch back to isdir to see if older octave is happier with this
Remi-Gau Oct 22, 2022
a0f08fe
Merge pull request #447 from Remi-Gau/doc
Remi-Gau Oct 22, 2022
d06a8ad
Merge remote-tracking branch 'origin/master' into dev
Remi-Gau Oct 29, 2022
2235c70
Merge branch 'master' into dev
Remi-Gau Oct 29, 2022
80f3bb9
Merge branch 'master' into dev
Remi-Gau Oct 29, 2022
926f94f
update README
Remi-Gau Oct 29, 2022
622f70c
Merge branch 'master' into dev
Remi-Gau Oct 30, 2022
9347215
update create participants.tsv
Remi-Gau Oct 30, 2022
dba140b
update image path
Remi-Gau Oct 30, 2022
94df0a2
Merge branch 'master' into dev
Remi-Gau Nov 3, 2022
06f2b8e
fix copyright line skip
Remi-Gau Nov 3, 2022
3efc8a9
Merge remote-tracking branch 'upstream/master' into dev
Remi-Gau Nov 4, 2022
711f546
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Nov 4, 2022
bbe75d5
fix spelling
Remi-Gau Nov 4, 2022
396a5bd
Merge remote-tracking branch 'origin/update' into update
Remi-Gau Nov 4, 2022
435e03f
fix report tests
Remi-Gau Nov 4, 2022
453230e
Merge pull request #459 from Remi-Gau/update
Remi-Gau Nov 4, 2022
f46e708
Merge branch 'master' into dev
Remi-Gau Nov 7, 2022
9c4452c
update create participants
Remi-Gau Nov 7, 2022
de43a2b
add create session tsv
Remi-Gau Nov 7, 2022
758cf57
fix test
Remi-Gau Nov 7, 2022
e9bcc02
update test
Remi-Gau Nov 7, 2022
630e3d0
update bids init
Remi-Gau Nov 7, 2022
46825c0
refactor create readme
Remi-Gau Nov 7, 2022
1723656
update create readme
Remi-Gau Nov 7, 2022
9230720
add extra columns sessions.tsv
Remi-Gau Nov 7, 2022
5fe0357
add doc arguments
Remi-Gau Nov 7, 2022
2395fd6
lint
Remi-Gau Nov 7, 2022
07f915d
improve test and messages
Remi-Gau Nov 7, 2022
b35592b
fix some test
Remi-Gau Nov 7, 2022
1907640
exclude some files from scans.tsv
Remi-Gau Nov 7, 2022
ed09c9b
refactor tests
Remi-Gau Nov 7, 2022
d2ad5e5
fix octave warning
Remi-Gau Nov 7, 2022
25b9b69
silence warning test on octave
Remi-Gau Nov 7, 2022
9631f4a
skip bids validation with octave for now
Remi-Gau Nov 8, 2022
c0c94a4
skip failing matlab test
Remi-Gau Nov 8, 2022
2b9c711
simplify test
Remi-Gau Nov 8, 2022
4cc8232
windows related fixes
Remi-Gau Nov 8, 2022
8a0071b
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Nov 8, 2022
2825fe1
Merge branch 'dev' into win_fix
Remi-Gau Nov 8, 2022
20a664a
Merge pull request #466 from Remi-Gau/win_fix
Remi-Gau Nov 8, 2022
66938e8
skip octave test
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d1615ae
Merge pull request #463 from Remi-Gau/update_dataset
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71f9212
Merge remote-tracking branch 'upstream/master' into dev
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f49f6e5
Merge remote-tracking branch 'upstream/master' into dev
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7bec8ca
improve error message
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1dc1874
fix octave test
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e9c47a4
Merge pull request #472 from bids-standard/error_msg
Remi-Gau Nov 9, 2022
de0db63
Merge branch 'master' into dev
Remi-Gau Nov 11, 2022
dd57984
fix listing of trial types
Remi-Gau Nov 13, 2022
bb5bd3a
improve default stats model when no task present
Remi-Gau Nov 13, 2022
4de02a1
silence test for warning under octave
Remi-Gau Nov 13, 2022
03b4077
Merge pull request #481 from bids-standard/list_trial_types
Remi-Gau Nov 13, 2022
74a7441
fix creation of json for derivatives when entity labels are numbers
Remi-Gau Nov 13, 2022
e9b108b
make download more robust
Remi-Gau Nov 13, 2022
257cafc
Merge pull request #484 from bids-standard/download
Remi-Gau Nov 13, 2022
e308d98
skip warning test for octave
Remi-Gau Nov 13, 2022
34d788e
Merge pull request #483 from bids-standard/derivatives
Remi-Gau Nov 13, 2022
72482a5
reformat windows path when printing to avoiding escaped characters wa…
Remi-Gau Nov 14, 2022
61f93e8
improve error message on query
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74bfd79
Merge remote-tracking branch 'origin/master' into win_path
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0f63858
Merge pull request #486 from bids-standard/win_path
Remi-Gau Nov 14, 2022
9b2db3f
fix create sessions and participants tsv
Remi-Gau Nov 16, 2022
9e0bd90
Merge pull request #487 from bids-standard/init_ses
Remi-Gau Nov 16, 2022
1876925
add potential datalad related hints when file writing fails
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157b2f7
Merge branch 'dev' into dev
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16c3c98
Merge pull request #488 from Remi-Gau/dev
Remi-Gau Nov 19, 2022
accfcc2
fix typo
Remi-Gau Nov 24, 2022
048c319
Merge remote-tracking branch 'origin/master' into typo
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6336a63
Merge pull request #491 from bids-standard/typo
Remi-Gau Nov 25, 2022
532a414
improve error message
Remi-Gau Nov 27, 2022
7fbd803
silence codespell
Remi-Gau Nov 27, 2022
ff52332
silence octave warning
Remi-Gau Dec 9, 2022
842673a
Merge branch 'new' into dev
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fd74a5b
Merge pull request #497 from bids-standard/master
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e8e006d
improve transformers
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83df308
Merge pull request #498 from bids-standard/trans
Remi-Gau Dec 13, 2022
857d13d
Merge remote-tracking branch 'origin/master' into dev
Remi-Gau Dec 26, 2022
0c27e2b
add response time histogram
Remi-Gau Dec 26, 2022
0f3491d
add get root node method
Remi-Gau Dec 26, 2022
bf34c36
refactor
Remi-Gau Dec 26, 2022
a0ac85c
use bids stats model to plot events
Remi-Gau Dec 26, 2022
e9f440f
fix code spell and octave bug
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f3689ec
fix miss hit config
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87f6c1d
remove comment
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f7bb51d
fix download face rep dataset
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d4fc82b
better handle datalad datasets
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15f174b
validate folder name in bids.init
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59bfe8e
fix cell indexing
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Merge pull request #503 from Remi-Gau/init
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21dbca5
Merge pull request #502 from Remi-Gau/datalad
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782a67e
fix cell indexing
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4570d92
update doc
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eabf771
Merge pull request #501 from bids-standard/events
Remi-Gau Dec 27, 2022
ceca48c
add diagnostic for events
Remi-Gau Dec 29, 2022
96929de
improve figure saving
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fa601d8
update doc
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61e8ac2
Merge pull request #504 from Remi-Gau/events_diag
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0984d59
rename transformers tests
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b946fc9
refactor tests
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a9b572a
silence writing tranformers test definitions
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5ac8db0
move logical operation as compute opertion
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0480e5e
update transformer test description
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f2730dd
update facerep
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b245358
Merge pull request #506 from Remi-Gau/transformer_rules
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0049c4f
Merge pull request #507 from bids-standard/facerep
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2eaeb13
add versbosity options to reports
Remi-Gau Jan 18, 2023
ec93e35
Merge branch 'master' into dev
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a53fcba
add flag to all figures
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46d1ab6
Merge pull request #509 from bids-standard/silence
Remi-Gau Jan 18, 2023
e2029f4
add filter to layout to only index certain subjects, sessions, modali…
Remi-Gau Jan 22, 2023
0855b9a
use filtering of layout
Remi-Gau Jan 22, 2023
9e05c94
fix when no filter
Remi-Gau Jan 22, 2023
bbfb6c8
use regexp
Remi-Gau Jan 22, 2023
d67d110
fix when to use regex
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3dfba0c
Merge pull request #510 from bids-standard/filter_layout
Remi-Gau Jan 22, 2023
43c156f
compat
CPernet Jan 30, 2023
fd5c4ab
all fmap not populated
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merge remote
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with files
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[pre-commit.ci] auto fixes from pre-commit.com hooks
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allow empty subject directories when going schema less
Remi-Gau committed Jun 8, 2022
commit 0c0a4a8d177477a19431339b09ef718fc2cb0002
8 changes: 8 additions & 0 deletions +bids/layout.m
Original file line number Diff line number Diff line change
@@ -241,9 +241,16 @@
% so the parsing is unconstrained
for iModality = 1:numel(modalities)
switch modalities{iModality}

case {'anat', 'func', 'beh', 'meg', 'eeg', 'ieeg', 'pet', 'fmap', 'dwi', 'perf', 'micr'}
subject = parse_using_schema(subject, modalities{iModality}, schema, verbose);

otherwise

if isempty(modalities{iModality})
continue
end

% in case we are going schemaless
% or the modality is not one of the usual suspect
if ~bids.internal.is_valid_fieldname(modalities{iModality})
@@ -258,6 +265,7 @@

subject.(modalities{iModality}) = struct([]);
subject = parse_using_schema(subject, modalities{iModality}, schema, verbose);

end
end

7 changes: 7 additions & 0 deletions tests/tests_layout/test_layout.m
Original file line number Diff line number Diff line change
@@ -6,6 +6,13 @@
initTestSuite;
end

function test_layout_empty_subject_folder_allowed_when_schemaless()
mkdir tmp;
mkdir tmp/sub-01;
bids.layout(fullfile(pwd, 'tmp'), 'use_schema', false);
rmdir(fullfile(pwd, 'tmp'), 's');
end

function test_layout_smoke_test()

pth_bids_example = get_test_data_dir();