[Freesurfer] Obtaining MNI-305 Coordinates for Destrieux ROIs

Hello,

I was following the conversation (recreated below) about converting the Destrieux ROI labels to MNI-305 coordinates and was wondering if all issues were resolved but not posted to the list. I attempted the same commands as were recommended in the original conversation:

*mri_annotation2label --subject fsaverage --hemi lh --annotation aparc.a2009s *

followed by

*mri_surfcluster --in fsaverage/surf/rh.thickness --clabel my_label.label --sum sum.my_label --centroid --thmin 0 --hemi lh --subject fsaverage --nofixmni *

*(where my_label is a given Destrieux ROI)* The 'sum' files returned by the second command all show the same MNI x-y-z coordinates as one another: [-29.4 -22.0 17.4] for lh ROIs and [29.8 -20.7 18.0] for rh ROIs. The original poster also said he observed that the x-y-z coordinates were the same for all of the ROIs for a given hemisphere. Like the original poster, I'm trying to get a single x-y-z MNI305-space coordinate triplet for each Destrieux ROI for use in network display software. Is there a modification to the above command that will return what I'm looking for?

The original conversation (italicized) is posted below in chronological order:

*Post #1: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg42598.html https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg42598.html*

*Hi Freesurfer Experts,

For the purpose of defining nodes in a graph theory analysis, I would like to generate a list of X Y Z coordinates in MNI space for all the labels in the Destrieux atlas. I came across a previous post with the following steps:*

*Step 1:

mri_annotation2label --subject fsaverage --hemi lh --annotation aparc.a2009s --outdir /Users/ElijahMak

Step 2:

mri_surfcluster --in /Applications/freesurfer/subjects/fsaverage/surf/lh.thickness --clabel lh.G_and_S_frontomargin.label --sum sum.lh.G_and_S_frontomargin --centroid --thmin 0 --hemi lh --subject fsaverage Everything went smoothly, but I would like to check my steps with you before I proceed to generate the coordinates individually for each ROI per hemisphere.

The output from #2 is sum.lh.G_and_S_frontomargin. When I load it, I see

dhcp-172-17-218-173:~ ElijahMak$ cat sum.lh.G_and_S_frontomargin

# Cluster Growing Summary (mri_surfcluster)

# $Id: mri_surfcluster.c,v 1.51.2.3 2012/05/31 22:10:05 greve Exp $

# $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $

# CreationTime 2015/08/10-12:29:31-GMT

# cmdline mri_surfcluster --in /Applications/freesurfer/subjects/fsaverage/surf/lh.thickness --clabel lh.G_and_S_frontomargin.label --sum sum.lh.G_and_S_frontomargin --centroid --thmin 0 --hemi lh --subject fsaverage

# cwd /Users/ElijahMak

# sysname Darwin

# hostname dhcp-172-17-218-173.eduroam.wireless.private.cam.ac.uk http://dhcp-172-17-218-173.eduroam.wireless.private.cam.ac.uk/

# machine x86_64

# FixVertexAreaFlag 1

# FixSurfClusterArea 1

#

# Input /Applications/freesurfer/subjects/fsaverage/surf/lh.thickness

# Frame Number 0

# srcsubj fsaverage

# hemi lh

# surface white

# SUBJECTS_DIR /Applications/freesurfer/subjects

# SearchSpace_mm2 65416.6

# SearchSpace_vtx 932

# Bonferroni 0

# Minimum Threshold 0

# Maximum Threshold infinity

# Threshold Sign abs

# AdjustThreshWhenOneTail 1

# Area Threshold 0 mm^2

# clabelfile lh.G_and_S_frontomargin.label

# clabelinv 0

# Overall max 3.33248 at vertex 83949

# Overall min 0 at vertex 0

# NClusters 1

# Total Cortical Surface Area 65416.6 (mm^2)

# FixMNI = 1

#

# ClusterNo Max VtxMax Size(mm^2) TalX TalY TalZ NVtxs

1 3.332 83949 82219.39 -29.4 -22.0 17.4 163842

Are those TalX TalY TalZ the values I'm looking for?

Many thanks for your time.

Best Wishes,

Elijah*

*Reply to Post #1: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg42656.html https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg42656.html*

*Those are more-or-less talairach coords, not MNI. If you add --nofixmni, the results will be reported in mni305 coords. - Douglas N Greve*

*Post #2: **https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg42693.html https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg42693.html*

*Hi Douglas,

Thanks for the help! However, when I tried the --nofixmni flag, all the ROIs appeared to have identical MNI coordinates. I have pasted the output from 3 ROIS in the LH.*

*# ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ NVtxs 1 3.332 83949 82219.39 -29.4 -22.0 17.4 163842 1 3.533 117158 82219.39 -29.4 -22.0 17.4 163842 1 3.170 83424 82219.39 -29.4 -22.0 17.4 163842

The same thing happens to the ROIs on the RH (XYZ: 29.8 29.8 18.0).

Best Wishes, *

*Elijah *

Thanks,

Riley