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

[Satrajit Ghosh]

hi,

in order to actually execute the command you will need to call
skullstrip.run(). you may need to set some other parameters to watershed to
get labeled output. you can also consider other routines like FAST from FSL
and AntsCorticalThickness from ANTS.

cheers,

satra

On Thu, Dec 7, 2017 at 7:42 AM, Supraja Jayakumar <suprajasankari at gmail.com>
wrote:

> 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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