Re: [Freesurfer] Segmentation Fault

It usually means that you have a subject whose surfaces are out-of-synch. This usually happens when you've made edits, launched recon-all, but then then recon-all does not finish for some reason. Check the time stamps on that subject or try running recon-all -make all -s subject

doug

btw, a "Segmentation Fault" is a computer term and does not have anything to do with brain segmentation.

Allie Rosen wrote:

Hi Bruce,

I mean the "mris_preproc" step.

Thanks, Allie

(forgot to reply to all)

On Tue, Apr 12, 2011 at 11:35 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> wrote:

Hi Allie,

what do you mean by "trying to assemble my subjects into a single
surface space"?

thanks
Bruce

On Tue, 12 Apr 2011, Allie Rosen wrote:

    Hi All,

    Upon trying to assembly my subjects into a single surface
    space, I got the
    following error:

    *ERROR: number of vertices in
    /media/AMMONIS/fsSubjects/AR_normals/C42/surf/lh.thickness
    does not match
    surface (142271,140585)
    ERROR: reading curvature file
    *
    I then tried to perform recon-all -make all, but got this error:

    *ERROR: mpr2mni305 failed, see transforms/talairach_avi.log*

    In the .log, I got this:

    *-7.5000   22.5000   15.0000 2793.2134   1Segmentation fault
    ERROR: 'imgreg_4dfp
    /usr/rapps/freesurfer/average/711-2C_as_mni_average_305
    /usr/rapps/freesurfer/average/711-2B_as_mni_average_305_mask
    talsrcimg_g11
    none talsrcimg_to_711-2C_as_mni_average_305_t4 4355' failed!
    status=139
    ERROR: mpr2mni305 execution aborted*

    Which is a segmentation fault. Can anyone help me fix this?

    Thanks,
    Allie Rosen, MSc Candidate
    Graduate Student, Department of Neurosurgery
    Toronto Western Hospital 14-327
    399 Bathurst St.
    University of Toronto



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