fix: FSL FNIRT intensity mapping files #1799
Merged
Conversation
This file contains hidden or 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
satra
reviewed
Feb 4, 2017
nipype/interfaces/fsl/preprocess.py
Outdated
| desc=('name of file/files containing initial ' | ||
| 'intensity maping usually generated by ' | ||
| 'previous fnirt run')) | ||
| in_intensitymap_file = traits.List(File, exists=True, argstr='--intin=%s', |
Codecov Report@@ Coverage Diff @@
## master #1799 +/- ##
==========================================
+ Coverage 69.82% 69.83% +<.01%
==========================================
Files 1047 1047
Lines 52050 52074 +24
Branches 7651 7658 +7
==========================================
+ Hits 36345 36364 +19
+ Misses 14127 14124 -3
- Partials 1578 1586 +8
Continue to review full report at Codecov.
|
|
@satra I've managed to get tests working, have test coverage for my new code, and have ensured that this fixes my problem. |
|
@satra thanks for the merge! |
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Outdated suggestions cannot be applied.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.
I've implemented the fix discussed in #1797, which changes intensity mapping files to be a list of outputs and inputs. Testing generated commands and outputs looks correct. commands look like
and files on disk are appropriately named (in this case,
oriented_structural_intmap.nii.gzandoriented_structural_intmap.txt). And outputs for my test cases match my expected outputs now, so this solves my issue. Thanks, @satra!closes #1797