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

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

# 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

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

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