Commit d91f6d2

author

Oweda

committed

FIX #3653: added option for using compressed files as inputs in CAT12 interface

1 parent 8c2a4ba commit d91f6d2Copy full SHA for d91f6d2

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lines changed

Lines changed: 6 additions & 2 deletions

Original file line number	Diff line number	Diff line change
`@@ -8,6 +8,7 @@`
`8`	`8`	`isdefined,`
`9`	`9`	`File,`
`10`	`10`	`Str,`
	`11`	`+ ImageFile,`
`11`	`12`	`)`
`12`	`13`	`from nipype.interfaces.cat12.base import Cell`
`13`	`14`
`@@ -23,7 +24,7 @@`
`23`	`24`
`24`	`25`	`class CAT12SegmentInputSpec(SPMCommandInputSpec):`
`25`	`26`	`in_files = InputMultiPath(`
`26`		`- ImageFileSPM(exists=True),`
	`27`	`+ ImageFile(exists=True),`
`27`	`28`	`field="data",`
`28`	`29`	`desc="file to segment",`
`29`	`30`	`mandatory=True,`
`@@ -559,6 +560,8 @@ def _format_arg(self, opt, spec, val):`
`559`	`560`	`"""Convert input to appropriate format for spm"""`
`560`	`561`	`if opt == "in_files":`
`561`	`562`	`if isinstance(val, list):`
	`563`	`+ if '.nii.gz' in val[0]:`
	`564`	`+ return scans_for_fnames(val, keep4d=True)`
`562`	`565`	`return scans_for_fnames(val)`
`563`	`566`	`else:`
`564`	`567`	`return scans_for_fname(val)`
`@@ -571,7 +574,8 @@ def _list_outputs(self):`
`571`	`574`	`outputs = self._outputs().get()`
`572`	`575`	`f = self.inputs.in_files[0]`
`573`	`576`	`pth, base, ext = split_filename(f)`
`574`		`-`
	`577`	`+ if '.nii.gz' in f:`
	`578`	`+ f = f[:-3]`
`575`	`579`	`outputs["mri_images"] = [`
`576`	`580`	`str(mri) for mri in Path(pth).glob("mri/*") if mri.is_file()`
`577`	`581`	`]`

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