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

it is necessary to do the aparc.a2009s. It should not be needed for wmparc (unless other files are not there)

On 1/10/14 8:08 PM, sujith vijayan wrote:

Hi Doug,

These were not done by me. What I have are the electrodes on top of MR images as well as their RAS coordinates (I sent you a screen shot before); done by registering a preop MRI with a postop CT scan. Is sphere.reg necessary for that?

Sujith

On Fri, Jan 10, 2014 at 7:21 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:

Hmmm, I think the sphere.reg has been there from the first version
of FS. If it is not there, then there is something wrong with that
recon. Have you used those recons for other purposes?



On 01/10/2014 07:12 PM, sujith vijayan wrote:

    Hi Doug,

    I double checked. The older recons do not have lh.sphere.reg
    in their surf folder or anywhere else it appears. The closest
    looking thing is a file called lh.qsphere.nofix. Pasted below
    are the contents of the surf directory (there are two columns).

    Sujith


    lh.afterrh.after

    lh.arearh.area

    lh.area.midrh.area.mid

    lh.area.pialrh.area.pial

    lh.beforerh.before

    lh.curvrh.curv

    lh.curv.pialrh.curv.pial

    lh.defect_bordersrh.defect_borders

    lh.defect_chullrh.defect_chull

    lh.defect_labelsrh.defect_labels

    lh.inflatedrh.inflated

    lh.inflated.Hrh.inflated.H

    lh.inflated.Krh.inflated.K

    lh.inflated.nofixrh.inflated.nofix

    lh.new_orig_uncorrectedrh.new_orig_uncorrected

    lh.new_qsphere_uncorrectedrh.new_qsphere_uncorrected

    lh.origrh.orig

    lh.orig.nofixrh.orig.nofix

    lh.pialrh.pial

    lh.qsphere.nofixrh.qsphere.nofix

    lh.smoothwmrh.smoothwm

    lh.smoothwm.nofixrh.smoothwm.nofix

    lh.sulcrh.sulc

    lh.thicknessrh.thickness

    lh.volumerh.volume

    lh.whiterh.white




    On Fri, Jan 10, 2014 at 6:11 PM, Douglas N Greve
    <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
    <mailto:greve@nmr.mgh.harvard.edu
    <mailto:greve@nmr.mgh.harvard.edu>>> wrote:

        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>
    <mailto:svijayan9@gmail.com <mailto:svijayan9@gmail.com>>
            <mailto:svijayan9@gmail.com
    <mailto:svijayan9@gmail.com> <mailto: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>
            <mailto:greve@nmr.mgh.harvard.edu
    <mailto:greve@nmr.mgh.harvard.edu>>
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    <mailto:greve@nmr.mgh.harvard.edu>

            <mailto: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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