It is not the dicom file but the rawavg.mgz that is the immediate problem.

As for the subject you sent, it is hard to say what is going wrong. It looks like there might be a lot of WM pathology. Is that right? That might be difficult for our intensity normalization. You can try placing control points in voxels that you are sure are WM (and not equal to 110 on the T1.mgz)

doug

On 02/20/2014 01:06 PM, Victor Kovac wrote:

Hi Doug,

I will would double-check the dcm files and re-run recon-all on that scan.

Attached are an image of the segmentation and the recon-all.log file from another timepoint of this subject. As you can see, a great deal of cortical gray and white matter is missed.

Thank you for your help! Victor

On Wed, Feb 19, 2014 at 4:26 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:

It looks like that file is corrupted. Is this disk full?


On 02/19/2014 05:21 PM, Victor Kovac wrote:

    Hi Doug.

    This is the output:
    $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
    reading from
    /lustre/kovacv/FS/post_analysis/MPS2005-2/mri/rawavg.mgz...
    mghRead(/lustre/kovacv/FS/post_analysis/MPS2005-2/mri/rawavg.mgz):
    could not read 131072 bytes at slice 150

    I was wondering if it might be that the dicom file
    corresponding to slice 150 was corrupted, so I checked slice
    150 in the sagittal plane, but I see no error.

    Please advise.

    Thanks!
    Victor


    On Wed, Feb 19, 2014 at 3:48 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:

        The log file you sent shows recon-all failing at a very early
        point before the issue with the PV spaces could become a
    problem.
        It appears to fail at this command-line.

        mri_convert
        /lustre/kovacv/FS/post_analysis/MPS2005-2/mri/rawavg.mgz
        /lustre/kovacv/FS/post_analysis/MPS2005-2/mri/orig.mgz
    --conform

        Can you run this and post the terminal output to the list



        On 02/19/2014 12:08 PM, Victor Kovac wrote:
        > Hello FreeSurfer experts,
        >
        > I have four scans from a subject who has ubiquitous, dilated
        > perivascular spaces (image attached) that seem to be
    preventing
        > recon-all from finishing. I have attached the
    recon-all.log from one
        > of the scans.
        >
        > Any advice on what I could try to get these scans
    analyzed would be
        > greatly appreciated.
        >
        > Thank you!
        > Victor
        >
        >
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