Hi Doug,
After resampling the aparc annotation into the functional native space, the LUT values no longer correspond to the correct regions. A screenshot is attached here: http://i.imgur.com/HNIgrKI.png
The values for the labels range from 1 - 35 only.
The command is mri_label2vol --annot $i/label/rh.aparc.annot --temp ${i}_medn.nii --reg $i/fmri/fmri_t1_mricoreg.dat --fillthresh 0.5 --hemi rh --subject $i --proj frac 0 .1 1 --o ${i}.rh.aparc.in.func.nii
The goal is to apply the annotation and extract the regional fMRI data (4D) using this 3D volume parcellation. Could we achieve that by using these steps?
Thanks.
Best Wishes, Elijah
On 13 June 2017 at 07:05:13, Douglas Greve (greve@nmr.mgh.harvard.edu) wrote:
You can try mri_concat seg1.nii.gz seg2.nii.gz --sum --o seg.nii.gz
This will work if there are no overlapping voxels. If there are, you'll have to do something like
mri_mask seg1.nii.gz seg2.nii.gz seg1-masked.nii.gz
then use the masked in the mri_concat command
On 6/11/17 11:18 AM, Elijah Mak wrote: Hi Freesurfer Team,
I am trying to resample the aparc annotation into functional space using mri_label2vol. It works fine and the script produced the segmentation for each hemisphere. Is there a way to merge both the left and right volumes together? Thanks for your help.
Best Wishes, Elijah
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