Hi Srishti
if you look in the subject's scripts dir there should be a file named
"recon-all.cmd". Try rerunning the last command in it (probably from the
mri dir)
cheers
Bruce
On Thu, 5 Apr 2018, srishti goel wrote:
I am sorry, I am not sure what do you mean by running the command line directly?
I use the following command:
sbatch --mem 2200 -t 6-00:00 --mail-type END --mail-user [email protected]
--wrap "export
SUBJECTS_DIR=/proj/hng/sheridanlab/freeSurfer/DukeYAS/Freesurfer_out/; recon-all -s
13166 -autorecon2-cp -autorecon3 -nowmsa"
where sbatch..... until export is our local server submission command and I run
this command from the command line itself, not
using any script.
Best,
Srishti
Social/Clinical Research Specialist
Child Imaging Research and Life Experiences Lab
University of North Carolina at Chapel Hill
email (W): [email protected]
skype: srishti.goel12
On Thu, Apr 5, 2018 at 12:24 PM, Bruce Fischl <[email protected]>
wrote:
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): [email protected]
skype: srishti.goel12
On Thu, Apr 5, 2018 at 12:16 PM, Bruce Fischl
<[email protected]>
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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