Re: [Freesurfer] wmparc.mgz and aparc.a2009s+aseg.mgz

I think there must be something else wrong because the sphere.reg has to be there. Did you check?

On 01/10/2014 06:08 PM, sujith vijayan wrote:

Is there a slightly earlier stage I could start at, such that I would not get an error?

Sujith

On Fri, Jan 10, 2014 at 2:42 PM, sujith vijayan <svijayan9@gmail.com mailto:svijayan9@gmail.com> wrote:

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 <mailto: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:
    >
    > 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
    >
    >
    >
    > _______________________________________________
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    --
    Douglas N. Greve, Ph.D.
    MGH-NMR Center
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