-
Notifications
You must be signed in to change notification settings - Fork 45
Add node to check for subject's Freesurfer directory #504
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.
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
Conversation
effigies
left a comment
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
I would suggest that we gate the other nodes on this passing, so have it do something like:
fs_params = [(field, field) for field in ('subjects_dir', 'subject_id')]
workflow.connect([
(inputnode, check_subjects_dir, fs_params),
(check_subjects_dir, fs_base_inputs, fs_params),
(check_subjects_dir, get_surfaces, fs_params),
(check_subjects_dir, save_midthickness, [
('subjects_dir', 'base_directory'),
('subject_id', 'container'),
]),
])IDC if you actually split out fs_params, I just didn't want to write it a bunch. Also, I'm realizing you could go ahead and collapse get_surfaces into fs_base_inputs/autorecon1, but that's a bit out of scope, so no worries if you don't want to.
|
Sure, I can do that. |
Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## master #504 +/- ##
==========================================
+ Coverage 70.88% 74.77% +3.88%
==========================================
Files 25 25
Lines 2068 2077 +9
Branches 268 270 +2
==========================================
+ Hits 1466 1553 +87
+ Misses 544 456 -88
- Partials 58 68 +10
Flags with carried forward coverage won't be shown. Click here to find out more. ☔ View full report in Codecov by Sentry. 🚀 New features to boost your workflow:
|
Closes #503.
Changes proposed:
init_surface_recon_wfthat is only called if--fs-no-resumeis used. This node checks if the subject's Freesurfer directory exists and raises an error if it does not.