FIX: replace the MRtrix3 command fs_parc_replace_sgm_first to labelsgmfix

[SheridanQ]

The MRtrix3 has renamed the fs_parc_replace_sgm_first to labelsgmfix

Summary

Fixes # .

List of changes proposed in this PR (pull-request)

Acknowledgment

• (Mandatory) I acknowledge that this contribution will be available under the Apache 2 license.

[effigies]

Was there a version where the old command was correct? If so, we should make the command depend on the version.

[SheridanQ]

Hi effigies,
I am new to the github, sorry that I didn't include this in my PR.
The last version where the old command was correct is version 0.3.13. After this version there was a major upgrade released on Mar 12 of 2016 that changed the command.

[effigies]

Okay, then we'll need to create a nipype.interfaces.mrtrix3.base.Info class that knows how to determine the version number. We can then select the correct command name based on whether the version is > 0.3.13.

@satra @mgxd Is there an existing example of an interface that has changed _cmd on version, or what would be the best model for this?

[mgxd]

After making an Info class for Mrtrix3 similar to the one below

nipype/nipype/interfaces/workbench/base.py

Lines 25 to 43 in 1ffe23d

	class Info(PackageInfo):
	"""
	Handle `wb_command` version information.
	"""
	version_cmd = 'wb_command -version'
	@staticmethod
	def parse_version(raw_info):
	m = re.search(r'\nVersion (\S+)', raw_info)
	return m.groups()[0] if m else None
	class WBCommand(CommandLine):
	"""Base support for workbench commands."""
	@property
	def version(self):
	return Info.version()

you can have a check in the interface's __init__ that can compare versions and change the _cmd, something like we do here

nipype/nipype/interfaces/c3.py

Lines 160 to 164 in 1ffe23d

	if self.inputs.is_4d:
	self._is_4d()
	def _is_4d(self):
	self._cmd = "c4d" if self.inputs.is_4d else "c3d"

@SheridanQ Lemme know if you have any questions/concerns!

[effigies]

Hi @SheridanQ. Just a bump on this. We're aiming to have the next release in about three weeks, so it'd be great to get this in within the next two weeks. Please let us know if you have any questions or need some further pointers.

[effigies]

Hi @SheridanQ. Please let us know if you need any help to finish this off.

[effigies]

Hi @SheridanQ, we're going to try to release 1.1.3 next Monday. Do you have time to finish this one up before then?

[effigies]

This pull request is "orphaned," which means it has been deemed to be abandoned by its original author. Orphaned pull requests have not been rejected, and we hope that if a user sees one that will meet their needs with a little work, that they will fork it and open a new pull request (or, in the case of the original author, reopen the original PR).

We ask that all adopted PRs be updated to merge or rebase the current master. If you would like to adopt a PR and need help getting started, any of a number of contributors will be happy to help.