Should I make up my own LUT for the new ROIs that specifies some colour and label number?
On Wed, Apr 9, 2014 at 10:00 AM, Corinna Bauer corinnab83@gmail.com wrote:
It looks like the FreeSurferColorLUT.txt does not contain the label number for the newly created labels (divided from the desikan atlas).
On Wed, Apr 9, 2014 at 9:53 AM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
$FREESURFER_HOME/FreeSurferColorLUT.txt
cheers Bruce On Wed, 9 Apr 2014, 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 <
greve@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 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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