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 (gr...@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
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine
at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and
properly
dispose of the e-mail.
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
