Fix mask output filename issues when '.nii.gz' is not included in out_fname #53
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
The current run_hd_bet function has a hard-coded string filter on the output mask name to append _mask.nii.gz to the output mask (line 78: mask_fname = out_fname[:-7] + "_mask.nii.gz"). However, if the user doesn't include the '.nii.gz' extension in the out_fname parameter, this will cause issues. For example, if out_fname is set to 'hd_bet_output', the resulting mask name will be 'hd_bet'. This update fixes this small bug and should work in both cases (i.e. where a user includes the '.nii.gz' extension, and those when the user doesn't include the '.nii.gz' extension).
bacaron
changed the title
bacaron
changed the title
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
The current run_hd_bet function has a hard-coded string filter on the output mask name to append _mask.nii.gz to the output mask (line 78: mask_fname = out_fname[:-7] + "_mask.nii.gz"). However, if the user doesn't include the '.nii.gz' extension in the out_fname parameter, this will cause issues. For example, if out_fname is set to 'hd_bet_output', the resulting mask name will be 'hd_bet.nii.gz'.
This update fixes this small bug and should work in both cases (i.e. where a user includes the '.nii.gz' extension, and those when the user doesn't include the '.nii.gz' extension).