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/talairach.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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