fslchfiletype

[Yasin Yazıcı]

Hi,

The code below is written for fslchfiletype function. It is very similar to other fsl commands in nipype folder. It works fine when out_file is specified. However, if out_file is not specified it raises an error like below

FileNotFoundError: File/Directory 'a directory in here' not found for FslChFileType output 'out_file'.
Interface FslChFileType failed to run.

The reason is if output is not specified fslchfiletype set output directory to current directory not to input`s (in_file) directory. So if the pipeline script is in a specific directory and in_file is not in the same directory (generally in tmp file), nipype can not find the output because it is searching the input directory.

class FslChFileTypeInputSpec(FSLCommandInputSpec):

    file_type = traits.Str(desc='file type', argstr='%s', position=0, mandatory=True)

    in_file = File(desc="input file", exists=True, argstr="%s", position=1, mandatory=True)

    out_file = File(genfile=True, desc="output file", argstr="%s", hash_files=False)

class FslChFileTypeOutputSpec(TraitedSpec):
    out_file = File(desc = "out file", exists = True)

class FslChFileType(FSLCommand):
    input_spec = FslChFileTypeInputSpec
    output_spec = FslChFileTypeOutputSpec
    cmd = 'fslchfiletype'

    def _list_outputs(self):
        outputs = self._outputs().get()
        ext = Info.output_type_to_ext(self.inputs.file_type)
        outputs['out_file'] = self.inputs.out_file
        if not isdefined(outputs['out_file']):
            outputs['out_file'] = self._gen_fname(self.inputs.in_file,ext = ext,change_ext=True)
        return outputs

    def _gen_filename(self, name):
        if name == "out_file":
            return self._list_outputs()["out_file"]
        return None

How can I solve this problem and is there any command in nipype corresponding to fslchfiletype?

Regards

[Satrajit Ghosh]

hi yasin,

add `copyfile=False` to the metadata for in_file, this will create a symbolic link to the file in the node's working directory.

depending on which filetypes you are converting between, you could also write a nibabel function.

cheers,

satra

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[Satrajit Ghosh]

hi yasin,

i just checked this with the current development version of nipype and it works fine. could you please test it with the current version?

cheers,

satra

[Yasin Yazıcı]

Hi Satra,

Yes, it works fine if out_file is not specified, however when it specified, the output is saved the current folder (pwd) of python. I have re-installed nipype recently,so I don't think its about the version. For now, I'm using output_datatype of some of the fsl functions to convert between ANALYZE and NIFTI.

Kind Regards

Yasin

 

[Satrajit Ghosh]

replace this line:

        if not isdefined(outputs['out_file']):
            outputs['out_file'] = self._gen_fname(self.inputs.in_file,ext =ext,change_ext=True)

with:

        if not isdefined(outputs['out_file']):
            outputs['out_file'] = self._gen_fname(self.inputs.in_file,ext =ext,change_ext=True)

        else:

            outputs['out_file'] = os.path.abspath(outputs['out_file'])

cheers,

satra

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