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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