And then for breaking the individual labels up, would mri_extract_label be
the best option?
On Wed, Jul 2, 2014 at 11:01 AM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
wrote:
> Hi Corinna
>
> you need to give some output extension so it knows what file type to write
> (e.g. .mgz, .nii, .nii.gz. mgh, ...)
>
> cheers
> Bruce
>
>
> On Wed, 2 Jul 2014, Corinna Bauer wrote:
>
> Hi Bruce,
>>
>> I am trying to do just that using the following command line:
>> mri_aparc2aseg --s ${subject} --labelwm --hypo-as-wm --rip-unknown
>> --volmask
>> --o ${subj_dir}/mri/wmdivided --annot aparc.split
>>
>> After the slice labeling, I get the following:
>>
>> Used brute-force search on 872 voxels
>> Fixing Parahip LH WM
>> Found 0 clusters
>> Fixing Parahip RH WM
>> Found 0 clusters
>> Writing output aseg to
>> /home/bauer/freesurfer_subjects/FSH_09062013/mri/wmdivided
>> unknown file type for file
>> (/home/bauer/freesurfer_subjects/FSH_09062013/mri/wmdivided)
>> subject = FSH_09062013
>> annotation = wmdivided
>> hemi = lh
>> outdir = /home/bauer/freesurfer_subjects/FSH_09062013/wm_hardi_labels
>> surface = white
>>
>> Any suggestions?
>>
>> Thanks,
>> Corinna
>>
>>
>>
>> On Tue, Jul 1, 2014 at 6:55 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
>> wrote:
>> Hi Corinna
>>
>> not really, as that is a surface-based utility. You could divide
>> the
>> cortical labels and then recrate the wmparc from it, which might
>> do what
>> you want.
>>
>> cheers
>> Bruce
>>
>>
>> On Tue, 1 Jul 2014, Corinna
>> Bauer wrote:
>>
>> > hello,
>> > I was wondering if it was possible to use
>> mris_divide_parcellation on white
>> > matter labels.
>> >
>> > Thanks,
>> >
>> > Corinna
>> >
>> >
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