let's see if it works. If it does, you should be able to run
recon-all -s SUBJID -make all
cheers
Bruce
On Thu, 5 Apr 2018, srishti goel wrote:
Should I re-run the recon-all after running the last command from recon-all.cmd?
Best,
Srishti
Social/Clinical Research Specialist
Child Imaging Research and Life Experiences Lab
University of North Carolina at Chapel Hill
email (W): srish...@email.unc.edu
skype: srishti.goel12
On Thu, Apr 5, 2018 at 12:31 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
wrote:
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
srish...@email.unc.edu --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): srish...@email.unc.edu
skype: srishti.goel12
On Thu, Apr 5, 2018 at 12:24 PM, Bruce Fischl
<fis...@nmr.mgh.harvard.edu> 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): srish...@email.unc.edu
skype: srishti.goel12
On Thu, Apr 5, 2018 at 12:16 PM, Bruce Fischl
<fis...@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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