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 greve@nmr.mgh.harvard.eduwrote:
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 <greve@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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