Skip to content
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

FIX: Clarify phase encoding direction, rather than axis #2302

Merged
merged 7 commits into from
Oct 12, 2020
Merged

FIX: Clarify phase encoding direction, rather than axis #2302

Changes from 1 commit
Commits
Show all changes
7 commits
Select commit Hold shift + click to select a range
de2cea4
FIX: Clarify phase encoding direction, rather than axis
mgxd Oct 9, 2020
832c734
FIX: Check image orientation
mgxd Oct 9, 2020
f0cad57
ENH: Incoporate @effigies' helper function
mgxd Oct 9, 2020
bfc26b3
ENH: Add source image orientation to summary report
mgxd Oct 9, 2020
fd932c9
TST: Add basic test
mgxd Oct 9, 2020
41c4c80
Update fmriprep/interfaces/reports.py
effigies Oct 10, 2020
c4fc08c
FIX: Skip if no PhaseEncodingDirection is found
mgxd Oct 12, 2020
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
10 changes: 6 additions & 4 deletions fmriprep/interfaces/reports.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -194,10 +194,12 @@ def _generate_segment(self):
'(boundary-based registration, BBR) - %d dof' % dof,
'FreeSurfer <code>mri_coreg</code> - %d dof' % dof],
}[self.inputs.registration][self.inputs.fallback]
if self.inputs.pe_direction is None:
pedir = 'MISSING - Assuming Anterior-Posterior'
else:
pedir = {'i': 'Left-Right', 'j': 'Anterior-Posterior'}[self.inputs.pe_direction[0]]
pedir = {
'i-': 'Left-Right',
'i': 'Right-Left',
'j-': 'Anterior-Posterior',
'j': 'Posterior-Anterior'
}.get(self.inputs.pe_direction, 'MISSING - Assuming Anterior-Posterior')
Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

This is only true for LAS images. We need the orientation of the original image, to be certain.

Copy link
Collaborator Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Good point - I've added a commit to consider LAS/RAS. How extensive do you think our support should be for different orientations?


if isdefined(self.inputs.confounds_file):
with open(self.inputs.confounds_file) as cfh:
Expand Down