if you run the command that failed again on the command line directly (that is, not in recon-all) does it fail again?
On Thu, 5 Apr 2018, srishti goel wrote:
Hi Bruce,
The machine definitely hasn't run out of memory. Here is the memory usage from recon-all.log
total used free shared buff/cache available Mem: 263726968 34330048 152102696 12944 77294224 191963372 Swap: 2097148 0 2097148
Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srishtig@email.unc.edu skype: srishti.goel12
On Thu, Apr 5, 2018 at 12:16 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Srishti
are you sure that your machine didn't just run out of memory? The recon-all.log file includes the amount of free (and total) memory at the time the process was started. cheers Bruce On Thu, 5 Apr 2018, srishti goel wrote: Hi, I have been trying to edit structural brains and very few times I would get the following error while running recon-all -s subjID white matter peak found at 110 cannot allocate memory Upon looking at the archive, there was only one similar issue and it was recommend to check mri_info as the brain mask might have been corrupted. I did that and here is the output: Volume information for brainmask.mgz type: MGH dimensions: 256 x 256 x 256 voxel sizes: 1.000000, 1.000000, 1.000000 type: UCHAR (0) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN FieldStrength: 0.000000 ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = -1.0000 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 37.5000 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = 4.7185 talairach xfm :/pine/scr/s/r/srishtig/Duke_Test/Freesurfer_out/11039/mri/transforms/talair ach.xfm Orientation : LIA Primary Slice Direction: coronal voxel to ras transform: -1.0000 0.0000 0.0000 127.0000 0.0000 0.0000 1.0000 -90.5000 0.0000 -1.0000 0.0000 132.7185 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant -1 ras to voxel transform: -1.0000 -0.0000 -0.0000 127.0000 -0.0000 -0.0000 -1.0000 132.7185 -0.0000 1.0000 -0.0000 90.5000 -0.0000 -0.0000 -0.0000 1.0000 Is there any other way to resolve this issue than reconstruction the brain again and doing all the edits all over again hoping that the brain mask does not get corrupted this time? Appreciate any help with this. Best, Srishti
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