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 <gr...@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:
> >
> > 1) 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.
> >
> > 2) 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
> >
> >
> >
> > _______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
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