you'll need to figure it out from the volume itself by loading the seg
with both -seg and -aux. When you find the label you want, click on it
and the aux value in the control window will tell you what the id is
doug
On 04/09/2014 09:41 AM, Corinna Bauer wrote:
> In the mri_extract_label, there is a label number. Where would I find
> this for the new labels?
>
> i.e. mri_extract_label ${subj_dir}/mri/aparc+aseg.mgz 2035
> ${subj_dir}/hardi_labels/ctx-rh-insula.nii
>
>
> On Tue, Apr 8, 2014 at 10:50 PM, Douglas Greve
> <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
> yep, exactly
>
>
> On 4/8/14 6:00 PM, Corinna Bauer wrote:
>> Hi Doug,
>> After I have the labels then in each subject's T1 space, I will
>> need to then put them into diffusion and resting state space.
>>
>> I already have scripts that put the parcellations into
>> subject-specific diffusion/resting state space (using bbregister,
>> tkregister2, mri_vol2vol (using the inverse registration from
>> bbregister to put the T1 into diffusion space), mri_extract_label
>> (extract labels from aparc+aseg.mgz), and then mri_label2vol
>> (register each of the extracted labels into diffusion space).
>> Would a similar approach work for the new labels?
>>
>> Corinna
>>
>>
>> On Tue, Apr 8, 2014 at 5:42 PM, Douglas N Greve
>> <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>>
>>
>> Exactly what you have described won't work very well because
>> it would be
>> in the volume. I would divide up the parcellations in
>> fsaverage space
>> like you've done, then map the parcellation to each subject using
>> mri_surf2surf (--sval-annot, see example 6)
>>
>> doug
>>
>> On 04/08/2014 04:54 PM, Corinna Bauer wrote:
>> > Hello all,
>> >
>> > I am planning to use mris_divide_parcellation to split the
>> Desikan
>> > atlas into smaller ROIs, but will need the new ROIs to be
>> consistent
>> > between subjects.
>> >
>> > Can I achieve this if I register each subject to fsaverage
>> space and
>> > then apply the inverse transform to the divided
>> parcellations (which
>> > are currently done on the fsaverage brain)?
>> >
>> > If so, for extracting each label, what would be used for
>> the label
>> > number?
>> > (i.e. mri_extract_label ${subj_dir}/mri/aparc+aseg.mgz *2035*
>> > ${subj_dir}/hardi_labels/ctx-rh-insula.nii)
>> >
>> >
>> > Thanks
>> >
>> > Corinna
>> >
>> >
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>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>
>> Phone Number: 617-724-2358 <tel:617-724-2358>
>> Fax: 617-726-7422 <tel:617-726-7422>
>>
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>>
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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