Re: [Freesurfer] error loading volume brainmask.gcut.mgz

is your disk partition full? And please cc the list so others can answer Bruce On Thu, 30 May 2013, Claudia Dacquino wrote:

Yes I did run mri_info, these are the results: Volume information for brainmask.gcuts.mgz           type: MGH     dimensions: 256 x 256 x 256    voxel sizes: 1.0000, 1.0000, 1.0000           type: INT (1)            fov: 256.000            dof: 0         xstart: -128.0, xend: 128.0         ystart: -128.0, yend: 128.0         zstart: -128.0, zend: 128.0             TR: 7.92 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees        nframes: 1        PhEncDir: UNKNOWN ras xform present     xform info: x_r =  -1.0000, y_r =   0.0000, z_r =  -0.0000, c_r =     8.4909               : x_a =  -0.0000, y_a =   0.0000, z_a =   1.0000, c_a =    -0.4031               : x_s =   0.0000, y_s =  -1.0000, z_s =  -0.0000, c_s =   -34.1638

talairach xfm :  Orientation   : LIA Primary Slice Direction: coronal

voxel to ras transform:                -1.0000   0.0000  -0.0000   136.4909                -0.0000   0.0000   1.0000  -128.4031                 0.0000  -1.0000  -0.0000    93.8362                 0.0000   0.0000   0.0000     1.0000

voxel-to-ras determinant -1

ras to voxel transform:                -1.0000  -0.0000  -0.0000   136.4909                -0.0000  -0.0000  -1.0000    93.8362                -0.0000   1.0000  -0.0000   128.4031                 0.0000   0.0000   0.0000     1.0000

Cheers

2013/5/30 Bruce Fischl fischl@nmr.mgh.harvard.edu did you run out of disk space? Can you run mri_info on it? On Thu, 30 May 2013, Claudia Dacquino wrote:

        Hi Freesurfers,I'm trying to remove some dura which
        affect my surfaces with
        the command 

        recon-all -skullstrip -clean-bm -gcut -subjid

        but then I can't use tkmedit to check that.
        The message I get is:

        Error: Loading volume brainmask.gcut.mgz Couldn't
        read the anatomical
        volume. Tkmedit couldn't read the volume you
        specified. This could be
        because the image format wasn't recognized, or it
        couldn't find the proper
        header, or the file(s) were unreadable, or it was
        the wrong size.
         
        Actually I did check in brainmask.gcut.mgz directory
        properties, and I saw
        the size of image is something like 150 KB, instead
        of 1 MB like is
        brainmask.mgz.

        What is the problem?

        Thanks,
        Claudia

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