Re: [Freesurfer] mri_vol2vol

why are you running xhemireg for fsaverage?

On 10/02/2012 06:04 PM, Andrew Bock wrote:

I updated all the xhemi scripts following: http://www.freesurfer.net/fswiki/Xhemi but unfortunately the problem persists for fsaverage, since norm.mgz does not exist for fsaverage. I'm going to try creating norm.mgz for fsaverage to see if xhemireg works. Even if it doesn't, xhemireg does work for my other subjects, so I'll be able to find a solution.

Thanks for your help,

Andrew

On Tue, Oct 2, 2012 at 12:19 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:

when did you update the xhemi scripts last? Do a search on our
wiki for xhemi to get pointers to the most recent ones


On 10/02/2012 01:59 PM, Andrew Bock wrote:

    Thanks Doug!

    However, now I'm getting the following error:

    /Resampling

    Output registration matrix is identity

    mri_vol2vol done
    ERROR: canot find norm/

    I am running:

    /xhemireg --s fsaverage --reg/


    Any suggestions? Should I run the following from
    $SUBJECTS_DIR/fsaverage/mri/?

    mri_nu_correct.mni --i orig.mgz --o nu.mgz --n 2 --uchar
    transforms/talairach.xfm
    mri_ca_normalize -mask brainmask.mgz nu.mgz
    $FREESURFER_HOME/average/RB_all_2008-03-26.gca
    transforms/talairach.lta norm.mgz

    Andrew


    On Mon, Oct 1, 2012 at 8:32 PM, Douglas 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 just put a new version here:

    ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_vol2vol

        doug



        On 10/1/12 10:56 PM, Andrew Bock wrote:

            Hello,

            I'm having a problem similar to the one outlined here:
        https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2012-June/024182.html

            When I run xhemireg I receive the error "ERROR: Option
            --keep-precision unknown"

            I looked for the newer version of mri_vol2vol
        described in the
            previous post, but could not find it on the ftp site.  Any
            suggestions?

            Andrew




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