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.