Hi Antonin and Thomas,
Thanks a lot for your reply.
I just wanted to confirm once again with you following steps. I ran: (1). mri_surf2surf --srcsubject fsaverage --trgsubject yoursubject --hemi lh --sval-annot lh.Yeo2011_7Networks_N1000.annot --tval $SUBJECTS_DIR/yoursubject/label/lh.Yeo_7Network_native.annot
(2). mri_segstats --annot my_subject_id lh lh.Yeo_7Network_native.annot --i $SUBJECTS_DIR/my_subject_id/surf/lh.pial_lgi --sum lh.aparc.pial_lgi.stats
These two steps are working fine and giving me 7 values in 'stats' file. These 7 values represent lgi values of 7 networks, is that correct? I am not sure why we do not need step mri_label2vol here as mentioned by Thomas. If I run mri_label2vol step, it requires reghead flag input, which I do not have.
Another question: If we do not need mri_label2vol step and steps (1) and (2) above are correct to get LGI values of 7 networks, could you please tell me how can I display LGI values (average over subjects) in fsaverage space for publication purpose?
Thanks a lot.
On Tue, Feb 14, 2017 at 8:45 PM, Thomas Yeo ythomas@csail.mit.edu wrote:
Hi Martin,
Sorry for the slow reply. Antonin is right about the mri_segstats.
To map the surface parcellation from fsaverage to your individual subject's anatomical space, you can do the following:
# Transform from fsaverage to subject's surface
mri_surf2surf --srcsubject fsaverage --trgsubject yoursubject --hemi lh
--sval-annot lh.Yeo2011_17Networks_N1000.annot --tval $SUBJECTS_DIR/yoursubject/label/lh.Yeo_17Network_native.annot
# Transform from subject's surface into your subject's volume (I am not super sure about this. You probably want to double check the output is correct)
mri_label2vol --annot lh.Yeo2011_17Networks_N1000.HS_001.annot --o
outfile.nii.gz --hemi lh --subject HS_001 --regheader
Regards, Thomas
On Sat, Feb 11, 2017 at 5:01 AM, Antonin Skoch ansk@ikem.cz wrote:
Dear Martin,
I think that this thread is relevant for you:
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg34508.html
You would have to map Yeo atlas to individual brain and then extract the
LGI
values using command:
mri_segstats --annot my_subject_id lh aparc --i $SUBJECTS_DIR/my_subject_id/surf/lh.pial_lgi --sum
lh.aparc.pial_lgi.stats
where aparc replace by name of your generated Yeo atlas annot file.
Regards,
Antonin Skoch
Hi everyone,
I was wondering if someone could please address the following question regarding FreeSurfer usage.
I would really appreciate any help.
Thanks.
Hi,
I used following command to extract LGI values from a set of subjects:
recon-all -s <subj> -localGI
Output stats is saved in lh.aparc_lgi.stats file. By default, its calculating LGI values of 35 areas using *Desikan-Killiany Atlas *but I
am
interested in calculating LGI values using Yeo atlas of 7 networks. I was wondering how can I change the default atlas to Yeo atlas to get LGI
value
for each subject.
Thanks a lot.
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