App overwriting output from _left and _right .nii.gz

[soichih]

I am trying to feed the output from TractSeg directly into to this App.

Previously, app-tractseg was generating output files named like the following.

R_Thalamo-precentral_Vol.nii.gz
R_Thalamo-prefrontal_Vol.nii.gz

Now, I am feeding file names like these - as generated by TractSeg

T_PREC_right.nii.gz
T_PREC_left.nii.gz
T_PREF_right.nii.gz
T_PREF_left.nii.gz

This app currently truncates the last part of the file name "_Vol or _right/_left" with the following code in main.py

    split_name = os.path.basename(file).split('_')
    split_name[-1] = 'surf.' + filetype
    surfname = '_'.join(split_name)

This means _right _left names are removed and ends up overwriting the output .vtk files - and generating about half as many output files as it should. To make this App more generic, can we update to leave the last token inside the output filename? (Or update it will only trim the last token if it's "_Vol"?)

[kitchell]

I accepted the pull request, but I think changes need to be done to deal with vol from the mask app

[soichih]

I just tested it with output from the Binary Tract Mask App. Apart from the surface names containing "_vol", it seems to work still. (I think "_Vol" should be removed on app-generatetractmasks).

The surface displayed upside down is a preexisting condition, I think.