[Neuroimaging] Segmentation of .nii file using WatershedSkullStrip()

[Supraja Jayakumar]

Hi.

I am trying to use the above API for segmenting .nii.gz (should i extract
it first?) files from the ABIDE datasets into white and grey matter. After
calling:

skullstrip.cmdline
'mri_watershed -T1 transforms/talairach_with_skull.lta T1.mgz
brainmask.auto.mgz'

The full code is here:

>
> from nipype.interfaces.freesurfer import WatershedSkullStrip
> skullstrip = WatershedSkullStrip()
> skullstrip.inputs.in_file =
> '/home/venkat/connectomes/datasets/abide_dparsf/ABIDE_pcp/dparsf/nofilt_noglobal/NYU_0050952_func_preproc.nii.gz'
> skullstrip.inputs.t1 = True
> skullstrip.inputs.transform = "transforms/talairach_with_skull.lta"
> skullstrip.inputs.out_file = "brainmask.auto.mgz"
> skullstrip.cmdline
> 'mri_watershed -T1 transforms/talairach_with_skull.lta T1.mgz
> brainmask.auto.mgz'
> # skullstrip.help()



I do not see any segmented images generated in the given out_file location.
I suppose i am not doing this the right way. Pls point out what's wrong in
the above code.

Thanks
S.Venkat

-- 
U
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