Skip to content

Updated RobustFOV API #1923

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 1 commit into from
Apr 20, 2017
Merged

Updated RobustFOV API #1923

Changes from all commits
Commits
Show all changes
1 commit
Select commit
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
14 changes: 14 additions & 0 deletions nipype/interfaces/fsl/utils.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -70,13 +70,27 @@ class RobustFOVInputSpec(FSLCommandInputSpec):
out_roi = File(desc="ROI volume output name", argstr="-r %s",
name_source=['in_file'], hash_files=False,
name_template='%s_ROI')
brainsize = traits.Int(170, desc='size of brain in z-dimension (default 170mm/150mm)',
argstr='-b %d', usedefault=False)
out_transform = File(desc="Transformation matrix in_file to out_roi output name", argstr="-m %s",
name_source=['in_file'], hash_files=False,
name_template='%s_to_ROI', usedefault=False, mandatatory=False)


class RobustFOVOutputSpec(TraitedSpec):
out_roi = File(exists=True, desc="ROI volume output name")
out_transform = File(exists=True, desc="Transformation matrix in_file to out_roi output name")


class RobustFOV(FSLCommand):
"""robustfov command has been introduced in FSL5. It automatically crops an
image removing lower head and neck.
Input of brainsize in optional (default 170mm/150mm)
Output of ROI and transformation matrix is optional.
Interface is stable 5.0.0 to 5.0.9
But default brainsize changed from 150mm to 170mm.
"""

_cmd = 'robustfov'
input_spec = RobustFOVInputSpec
output_spec = RobustFOVOutputSpec
Expand Down