Merged

ENH: added 'hsvs' option to 5ttgen + mrtransform fix #3630

Show file tree
Hide file tree
Changes from 3 commits
Show all changes
5 commits
Select commit Hold shift + click to select a range
3afcd62
Update utils.py
teanijarvFeb 20, 2024
367776d
Update .zenodo.json
teanijarvFeb 20, 2024
c08e17b
Update utils.py
teanijarvFeb 20, 2024
eda6497
Fix generate5tt input
teanijarvFeb 28, 2024
7fc44fd
Remove the -inverse parameter position change
teanijarvFeb 28, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Jump to
Failed to load files.
Original file line numberDiff line numberDiff line change
Expand Up@@ -224,13 +224,14 @@ class Generate5ttInputSpec(MRTrix3BaseInputSpec):
"fsl",
"gif",
"freesurfer",
"hsvs",
argstr="%s",
position=-3,
mandatory=True,
desc="tissue segmentation algorithm",
)
in_file = File(
exists=True, argstr="%s", mandatory=True, position=-2, desc="input image"
exists=False, argstr="%s", mandatory=True, position=-2, desc="input image"
Copy link
Member

Choose a reason for hiding this comment

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

So it seems like you need either a file or a directory, not a missing file.

in_file = traits.Either(
    File(exists=True),
    Directory(exists=True),
    argstr="%s", mandatory=True, position=-2, desc="input image / directory"
)

Copy link
Contributor Author

Choose a reason for hiding this comment

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

Thanks! I added this solution now. :)

)
out_file = File(argstr="%s", mandatory=True, position=-1, desc="output image")

Expand DownExpand Up@@ -822,7 +823,7 @@ class MRTransformInputSpec(MRTrix3BaseInputSpec):
)
invert = traits.Bool(
argstr="-inverse",
position=1,
position=2,
Copy link
Member

Choose a reason for hiding this comment

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

This means -invert will appear after all of the things with position=1. Does it need to come last, before in_files/out_file?

Copy link
Contributor Author

Choose a reason for hiding this comment

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

I removed the position change for now, but I just added this previously because if I wanted to use -inverse with some other parameter and they both had 'position=1' then only one would show up on the command. But it can also be fixed by just using inputs.args string.

desc="Invert the specified transform before using it",
)
linear_transform = File(
Expand Down