Skip to content

demo for using mean functional image mask #353

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
merged 9 commits into from
Jun 14, 2021
Merged

demo for using mean functional image mask #353

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
9 commits
Select commit Hold shift + click to select a range
8315013
add mean func mask into workflow
CerenB Apr 12, 2021
d699cfa
fix functional image input
CerenB Apr 12, 2021
8fa2d4d
reimplement demo
Remi-Gau Apr 13, 2021
d9736f1
mh fix
Remi-Gau Apr 13, 2021
fb13f01
update set up workflow
Remi-Gau Apr 13, 2021
600af63
make and save all possible masks
CerenB Apr 26, 2021
ce12187
mh fix
CerenB Apr 26, 2021
590883b
mh fix
Remi-Gau Jun 14, 2021
531ac49
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jun 14, 2021
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
25 changes: 14 additions & 11 deletions demos/MoAE/moae_run.m
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -27,26 +27,29 @@
bidsCopyRawFolder(opt, 1);

% In case you just want to run segmentation and skull stripping
% bidsSegmentSkullStrip(opt);
%
% NOTE: skull stripping is also included in 'bidsSpatialPrepro'
bidsSegmentSkullStrip(opt);

bidsSTC(opt);

bidsSpatialPrepro(opt);

% The following do not run on octave for now (because of spmup)
anatomicalQA(opt);
bidsResliceTpmToFunc(opt);
functionalQA(opt);

% anatomicalQA(opt);
% bidsResliceTpmToFunc(opt);
% functionalQA(opt);

% create a whole brain functional mean image mask
% so the mask will be in the same resolution/space as the functional images
% one may not need it if they are running bidsFFX
% since it creates a mask.nii by default
opt.skullstrip.mean = 1;
mask = bidsWholeBrainFuncMask(opt);

% smoooth the funcitional images
bidsSmoothing(FWHM, opt);

% The following crash on CI
WD = pwd;
% The following crash on Travis CI
bidsFFX('specifyAndEstimate', opt, FWHM);
cd(WD);
bidsFFX('contrasts', opt, FWHM);
cd(WD);
bidsResults(opt, FWHM);
cd(WD);
Loading