Re: [Freesurfer] v5.2.0 preproc-sess failing on 3dvolreg.afni

which version of CentOS? Also, can you send me the result of cat $FREESURFER_HOME/build-stamp.txt

On 03/21/2013 02:09 PM, Y.V. Jiang wrote:

Hi Doug,

I am using Linux: x86_64 GNU/Linux. Thanks.

-Yuhong

On Thu, Mar 21, 2013 at 12:57 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:

what platform are you using?


On 03/21/2013 01:24 PM, Y.V. Jiang wrote:

    Hi Doug,

    Thanks for the reply. From the command line the command
    3dvolreg.afni returned the following error:

    3dvolreg.afni: symbol lookup error: 3dvolreg.afni: undefined
    symbol: afni_ncerr

    -Yuhong

    On Thu, Mar 21, 2013 at 12:08 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:


        Hi Yuhong,
        What happens when you run 3dvolreg.afni from the command
    line without
        any args?
        doug

        On 03/21/2013 12:38 PM, Y.V. Jiang wrote:
        > Hi Doug,
        >
        > I was running preproc-sess in the newly released
        freesurfer-5.2.0. The
        > command I used was:
        >
        > preproc-sess -sf sessid -df sessdir -fsd bold -surface
    fsaverage lhr
        > -mni305 -fwhm 6 -per-run
        >
        > The program failed with the following errors:
        >
        > 3dvolreg.afni -verbose -dfile 004/fmcpr.mcdat -1Dmatrix_save
        > 004/fmcpr.mat -base
    004/tmp.mc-afni2.29239/tempvol.nii.gz -prefix
        > 004/tmp.mc-afni2.29239/outvol.nii.gz
        004/tmp.mc-afni2.29239/invol.nii.gz
        > 3dvolreg.afni: symbol lookup error: 3dvolreg.afni:
    undefined symbol:
        > afni_ncerr
        > ERROR: 3dvolreg.afni
        > Invalid null command.
        >
        > I have the file 3dvolreg.afni in $FREESURFER_HOME/bin.
    There is
        > another file of the same name under afni/bin.
    Preproc-sess is
        relying
        > on the version in $FREESURFER_HOME/bin.
        >
        > Do you know what the problem is? Should I replace
    freesurfer's
        copy of
        > 3dvolreg.afni with AFNI's copy of 3dvolreg.afni?
        >
        > Thanks.
        >
        > -Yuhong
        >
        >
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