Hi All,
I tried the command you suggested Doug (recon-all -s subject -wmparc -cortparc2 -aparc2aseg). It exits with an error because it cannot find the lh.sphere.reg file. The command and what is displayed after the command is executed is pasted below.
Sujith
recon-all -s MG24_SurferOutput -wmparc -cortparc2 -aparc2aseg
INFO: FreeSurfer build stamps do not match
Subject Stamp: freesurfer-Linux-centos4-stable-v4.0.5-20081003
Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0
INFO: SUBJECTS_DIR is /Volumes/Bach_III/New_Data/Duplicate
Actual FREESURFER_HOME /Applications/freesurfer
-rwxrwxrwx@ 1 sujithvijayan staff 529281 Oct 8 2008 /Volumes/Bach_III/New_Data/Duplicate/MG24_SurferOutput/scripts/recon-all.log
Darwin Sujiths-MacBook-Air.local 13.0.0 Darwin Kernel Version 13.0.0: Thu Sep 19 22:22:27 PDT 2013; root:xnu-2422.1.72~6/RELEASE_X86_64 x86_64
INFO: current FREESURFER_HOME does not match that of previous processing.
Current: /Applications/freesurfer
Previous: /usr/local/freesurfer/stable4
#-----------------------------------------
#@# Cortical Parc 2 lh Fri Jan 10 14:32:37 EST 2014
/Volumes/Bach_III/New_Data/Duplicate/MG24_SurferOutput/scripts
\n mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 MG24_SurferOutput lh ../surf/lh.sphere.reg /Applications/freesurfer/average/lh.destrieux.simple.2009-07-29.gcs ../label/lh.aparc.a2009s.annot \n
setting seed for random number generator to 1234
using ../mri/aseg.mgz aseg volume to correct midline
$Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $
$Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
MRISreadVertexPosition(../surf/lh.sphere.reg): could not open file ../surf/lh.sphere.reg
reading atlas from /Applications/freesurfer/average/lh.destrieux.simple.2009-07-29.gcs...
reading color table from GCSA file....
average std = 3.9 0.2 using min determinant for regularization = 0.000
0 singular and 1066 ill-conditioned covariance matrices regularized
No such file or directory
mris_ca_label: could not read spherical coordinate system from ../surf/lh.sphere.reg for MG24_SurferOutput
No such file or directory
On Fri, Jan 10, 2014 at 11:54 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu
wrote:
On 01/10/2014 11:40 AM, sujith vijayan wrote:
Hi All
I am using wmparc.mgz and aparc.a2009s+aseg.mgz to determine the closest grey matter region for electrodes in some human epileptic patients; I have the RAS coordinates of the electrodes. I have a couple of questions:
- When the electrode (its RAS coordinate) is close to the midline and
out of the grey matter it won't give me the closest grey matter label (like wmparc does with the white matter). Is there someway to get this in a principled manner? For example, is there a way to get a file with all the RAS coordinates and the parcellation labels, so I could find the closest neighbor in Matlab?
If you make a label file with the surface RAS coordinates of the electrodes, you can run run mri_label2label specifying the same subject as the source and target and --regmethod surface and --paint and it will map the points to the closest surface point.
- The recons for three subjects were done between 2008 and 2010 using
freesurfer. Therefore files like aparc.a2009s+aseg.mgz, wmparc.mgz, lh.aparc.a2009s.annot are missing. Is there a simple way just to recreate these set of files (one command would be great, even if it takes a little bit of time)? Or does the entire recon have to be done again?
If you have an installation of FS 5.3, you can run recon-all -s subject -wmparc -cortparc2 -aparc2aseg I think this will work on a 5.0 folder. I would make a copy of your subject before running it. It will regenerate the aparc+aseg.mgz file
doug
Thanks,
Sujith
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