error in dmri_mrtrix_dti.py example

[mekman]

I had to add

fsl.FSLCommand.set_default_output_type('NIFTI')

to this code example
http://www.mit.edu/~satra/nipype-nightly/users/examples/dmri_mrtrix_dti.html

otherwise I would get the following error. It seams that gen_WM_mask can't handle compressed nifti's?

gen_WM_mask -grad /home/matekm/dev/nipype-0.7/dmri_mrtrix_dti/dwiproc/tractography/_subject_id_subj1/fsl2mrtrix/bvecs_bvals.txt /home/matekm/dev/nipype-0.7/dmri_mrtrix_dti/dwiproc/tractography/_subject_id_subj1/gunzip/data.nii /home/matekm/dev/nipype-0.7/dmri_mrtrix_dti/dwiproc/tractography/_subject_id_subj1/bet_b0/data_brain_mask.nii.gz data_WMProb.mif
Standard output:

Standard error:
gen_WM_mask: unknown format for image "/home/matekm/dev/nipype-0.7/dmri_mrtrix_dti/dwiproc/tractography/_subject_id_subj1/bet_b0/data_brain_mask.nii.gz"
gen_WM_mask: error opening image "/home/matekm/dev/nipype-0.7/dmri_mrtrix_dti/dwiproc/tractography/_subject_id_subj1/bet_b0/data_brain_mask.nii.gz"
Return code: 1
Interface GenerateWhiteMatterMask failed to run.

[swederik]

Hmm indeed. I made the same issue almost a year ago. I'll make a short PR now and we can figure out how to deal with it properly later on.