can you email us the input file and the full command line you ran?
On Thu, 5
Apr 2018, srishti goel wrote:
So it gave this error:
3d normalization pass 1 of 2
white matter peak found at 110
HISTOalloc(-2147483648): could not allocate histogram
Cannot allocate memory
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 12:43 PM, Bruce Fischl <[email protected]>
wrote:
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): [email protected]
skype: srishti.goel12
On Thu, Apr 5, 2018 at 12:31 PM, Bruce Fischl
<[email protected]> 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 [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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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
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The information in this e-mail is intended only for the person to whom it is
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contains patient information, please contact the Partners Compliance HelpLine at
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