[ENH] Enable cnr_maps and residuals outputs for FSL eddy #2750
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nipype/interfaces/fsl/epi.py
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| @@ -659,6 +659,8 @@ class EddyInputSpec(FSLCommandInputSpec): | |||
| "the field specified by --field and first volume " | |||
| "in file --imain") | |||
| use_cuda = traits.Bool(False, desc="Run eddy using cuda gpu") | |||
| cnr_maps = traits.Bool(False, desc='Output CNR-Maps', argstr='--cnr_maps') | |||
| residuals = traits.Bool(False, desc='Output Residuals', argstr='--residuals') | |||
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Do we know if these were introduced in a particular version? If so, we should set the min_ver flag.
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I added 5.0.10 as the minimum version since this is the one i am using and that is working (despite the parameters not showing in the usage page). I messaged eddy's developers and they said that these parameters are actually planned to be released with eddy 6.0.1, they did not yet answer why the parameters are already usable in lower versions.
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Please merge master to fix tests. |
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Just a heads up: We're looking to make the next release on Nov 26, if you want to try to get this in this month. |
Codecov Report
@@ Coverage Diff @@
## master #2750 +/- ##
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+ Coverage 67.46% 67.48% +0.01%
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Files 341 341
Lines 43331 43343 +12
Branches 5371 5375 +4
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+ Hits 29235 29248 +13
+ Misses 13396 13388 -8
- Partials 700 707 +7
Continue to review full report at Codecov.
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effigies
changed the title
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Looks good.
Want to add your name, affiliation and ORCID to the .zenodo.json file?
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No thanks, maybe when i contribute something bigger than a couple of lines ;) |
1.1.7 (December 17, 2018) * FIX: Copy node list before generating a flat graph (nipy#2828) * FIX: Update pytest req'd version to 3.6 (nipy#2827) * FIX: Set ResourceMonitor.fname to an absolute path (nipy#2824) * FIX: Order of SPM.NewSegment channel_info boolean tuple is (Field, Corrected) (nipy#2817) * FIX: Indices were swapped for memory and cpu profile data (nipy#2816) * FIX: ``status_callback`` not called with ``stop_on_first_crash`` (nipy#2810) * FIX: Change undefined ScriptError on LFS plugin to IOError (nipy#2803) * ENH: Add NaN failure mode to CompCor interfaces (nipy#2819) * ENH: Enable cnr_maps and residuals outputs for FSL eddy (nipy#2750) * ENH: Improve ``str2bool`` + doctests (nipy#2807) * TST: Improve py.test configuration of doctests (nipy#2802) * DOC: Update DOI badge to point to all versions (nipy#2804) * MAINT: Offload interfaces with help formatting (nipy#2797) * MAINT: Reduce minimal code redundancy in filemanip.get_dependencies (nipy#2782) * MAINT: Delayed imports to reduce import time (nipy#2809) ...
Summary
Add the parameters 'cnr_maps' and 'residuals' to FSL eddy interface.
Fixes #2744 .
List of changes proposed in this PR (pull-request)
The outputs are only listed in _list_outputs if the input flags are defined and set to True.
The tests do not run on my work system since i cannot install all requirements.
I added the parameters to the test_auto_Eddy anyway since they are similar to --repol
I tested this manually with FSL version 5.0.10 .
--cnr_maps and --residuals do not show up in eddy's usage page but they work and are explained in the UserGuide:
https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/eddy/UsersGuide
Acknowledgment