Interface SPM ApplyTransform generated an error if out_file was not provided

[mick-d]

Generation of out_file name was broken and out_file remained empty if not provided, leading SPM to fail.

[chrisgorgo]

any chance we could use name_source here instead of genfilename?

[mick-d]

Sure, i'll just need to go back and check the exact use of name_source

[mick-d]

@chrisfilo what you are asking relies on refactoring the SPM base interface to add support for name_source

I tried but couldn't get it to work, for some reasons when debugging, the following commands in _parse_inputs:

metadata = dict(field=lambda t: t is not None) self.inputs.traits(**metadata).items() 

returns an empty list, with self.inputs.traits evaluating to:

self.inputs.traits <bound method MatlabInputSpec.traits of args = <undefined> environ = {} ignore_exception = False logfile = <undefined> mfile = True nodesktop = True nosplash = True paths = <undefined> postscript = ['\n,catch ME,', "fprintf(2,'MATLAB code threw an exception:\\n');", "fprintf(2,'%s\\n',ME.message);", "if length(ME.stack) ~= 0, fprintf(2,'File:%s\\nName:%s\\nLine:%d\\n',ME.stack.file,ME.stack.name,ME.stack.line);, end;", 'end;'] prescript = ["fprintf(1,'Executing %s at %s:\\n',mfilename,datestr(now));", 'ver,', 'try,'] script = infile = '/test/T1.nii'; outfile = '<undefined>' transform = load('/test/T1.mat'); V = spm_vol(infile); X = spm_read_vols(V); [p n e v] = spm_fileparts(V.fname); V.mat = transform.M * V.mat; V.fname = fullfile(outfile); spm_write_vol(V,X); script_file = pyscript_applytransform.m single_comp_thread = True terminal_output = allatonce uses_mcr = <undefined> > 

[mick-d]

Do you know why that would be?

[chrisgorgo]

I see. I'll add name_source support to BaseInterface later. For now you can stick with genfile.