Hello,
When I run the command "mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon --save_distance DK1" I get the following error:
ERROR: opening pipe gzip -f -c > /home/hammer/a/gonzalj/MirrorNeurons//DK1/mri/lh.dpial.ribbon.mgz, errno = 12 Cannot allocate memory mghWrite(/home/hammer/a/gonzalj/MirrorNeurons//DK1/mri/lh.dpial.ribbon.mgz, -1): could not open file
I had this error on a previous step and managed to solve it by means of using directories with COR files instead of a single mgz file for input and output. I do not see any option in mris_volmask to force it to write each COR file independently instead of a single .mgz file. How can I do this so I do not run into a memory problem? Also, any other ideas?
Thanks a lot,
Javier.
Javier,
It should not be necessary to revert to using COR files. How much memory and disk space do you have? We recommend 2GB of ram (and make sure disk space is not empty...freesurfer can fill-up a disk quickly).
Nick
On Wed, 2008-03-05 at 10:28 -0500, gonzalj@purdue.edu wrote:
Hello,
When I run the command "mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon --save_distance DK1" I get the following error:
ERROR: opening pipe gzip -f -c > /home/hammer/a/gonzalj/MirrorNeurons//DK1/mri/lh.dpial.ribbon.mgz, errno = 12 Cannot allocate memory mghWrite(/home/hammer/a/gonzalj/MirrorNeurons//DK1/mri/lh.dpial.ribbon.mgz, -1): could not open file
I had this error on a previous step and managed to solve it by means of using directories with COR files instead of a single mgz file for input and output. I do not see any option in mris_volmask to force it to write each COR file independently instead of a single .mgz file. How can I do this so I do not run into a memory problem? Also, any other ideas?
Thanks a lot,
Javier. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Nick,
I checked disk space and there are still 59G available, so that should not be the problem.
About RAM this system has 3GB.
Any idea of what might be going on?
Thanks a lot,
Javier.
Quoting Nick Schmansky nicks@nmr.mgh.harvard.edu:
Javier,
It should not be necessary to revert to using COR files. How much memory and disk space do you have? We recommend 2GB of ram (and make sure disk space is not empty...freesurfer can fill-up a disk quickly).
Nick
On Wed, 2008-03-05 at 10:28 -0500, gonzalj@purdue.edu wrote:
Hello,
When I run the command "mris_volmask --label_left_white 2
--label_left_ribbon 3
--label_right_white 41 --label_right_ribbon 42 --save_ribbon
--save_distance
DK1" I get the following error:
ERROR: opening pipe gzip -f -c > /home/hammer/a/gonzalj/MirrorNeurons//DK1/mri/lh.dpial.ribbon.mgz, errno =
12
Cannot allocate memory mghWrite(/home/hammer/a/gonzalj/MirrorNeurons//DK1/mri/lh.dpial.ribbon.mgz,
-1):
could not open file
I had this error on a previous step and managed to solve it by means of
using
directories with COR files instead of a single mgz file for input and
output. I
do not see any option in mris_volmask to force it to write each COR file independently instead of a single .mgz file. How can I do this so I do not
run
into a memory problem? Also, any other ideas?
Thanks a lot,
Javier. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Javier,
Which gzip version is being used? (gzip --version)
Nick
On Wed, 2008-03-05 at 11:54 -0500, gonzalj@purdue.edu wrote:
Hi Nick,
I checked disk space and there are still 59G available, so that should not be the problem.
About RAM this system has 3GB.
Any idea of what might be going on?
Thanks a lot,
Javier.
Quoting Nick Schmansky nicks@nmr.mgh.harvard.edu:
Javier,
It should not be necessary to revert to using COR files. How much memory and disk space do you have? We recommend 2GB of ram (and make sure disk space is not empty...freesurfer can fill-up a disk quickly).
Nick
On Wed, 2008-03-05 at 10:28 -0500, gonzalj@purdue.edu wrote:
Hello,
When I run the command "mris_volmask --label_left_white 2
--label_left_ribbon 3
--label_right_white 41 --label_right_ribbon 42 --save_ribbon
--save_distance
DK1" I get the following error:
ERROR: opening pipe gzip -f -c > /home/hammer/a/gonzalj/MirrorNeurons//DK1/mri/lh.dpial.ribbon.mgz, errno =
12
Cannot allocate memory mghWrite(/home/hammer/a/gonzalj/MirrorNeurons//DK1/mri/lh.dpial.ribbon.mgz,
-1):
could not open file
I had this error on a previous step and managed to solve it by means of
using
directories with COR files instead of a single mgz file for input and
output. I
do not see any option in mris_volmask to force it to write each COR file independently instead of a single .mgz file. How can I do this so I do not
run
into a memory problem? Also, any other ideas?
Thanks a lot,
Javier. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The output of gzip --version is:
gzip 1.3.12 Copyright (C) 2007 Free Software Foundation, Inc. Copyright (C) 1993 Jean-loup Gailly. This is free software. You may redistribute copies of it under the terms of the GNU General Public License http://www.gnu.org/licenses/gpl.html. There is NO WARRANTY, to the extent permitted by law.
Written by Jean-loup Gailly.
Javier.
Quoting Nick Schmansky nicks@nmr.mgh.harvard.edu:
Javier,
Which gzip version is being used? (gzip --version)
Nick
On Wed, 2008-03-05 at 11:54 -0500, gonzalj@purdue.edu wrote:
Hi Nick,
I checked disk space and there are still 59G available, so that should not
be
the problem.
About RAM this system has 3GB.
Any idea of what might be going on?
Thanks a lot,
Javier.
Quoting Nick Schmansky nicks@nmr.mgh.harvard.edu:
Javier,
It should not be necessary to revert to using COR files. How much memory and disk space do you have? We recommend 2GB of ram (and make sure disk space is not empty...freesurfer can fill-up a disk quickly).
Nick
On Wed, 2008-03-05 at 10:28 -0500, gonzalj@purdue.edu wrote:
Hello,
When I run the command "mris_volmask --label_left_white 2
--label_left_ribbon 3
--label_right_white 41 --label_right_ribbon 42 --save_ribbon
--save_distance
DK1" I get the following error:
ERROR: opening pipe gzip -f -c > /home/hammer/a/gonzalj/MirrorNeurons//DK1/mri/lh.dpial.ribbon.mgz,
errno =
12
Cannot allocate memory
mghWrite(/home/hammer/a/gonzalj/MirrorNeurons//DK1/mri/lh.dpial.ribbon.mgz,
-1):
could not open file
I had this error on a previous step and managed to solve it by means
of
using
directories with COR files instead of a single mgz file for input and
output. I
do not see any option in mris_volmask to force it to write each COR
file
independently instead of a single .mgz file. How can I do this so I do
not
run
into a memory problem? Also, any other ideas?
Thanks a lot,
Javier. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Javier,
Does mri_convert output .mgz files? What OS is being used? If mri_convert doesnt produce .mgz files, then I don't know what to suggest.
Nick
On Wed, 2008-03-05 at 12:22 -0500, gonzalj@purdue.edu wrote:
The output of gzip --version is:
gzip 1.3.12 Copyright (C) 2007 Free Software Foundation, Inc. Copyright (C) 1993 Jean-loup Gailly. This is free software. You may redistribute copies of it under the terms of the GNU General Public License http://www.gnu.org/licenses/gpl.html. There is NO WARRANTY, to the extent permitted by law.
Written by Jean-loup Gailly.
Javier.
Quoting Nick Schmansky nicks@nmr.mgh.harvard.edu:
Javier,
Which gzip version is being used? (gzip --version)
Nick
On Wed, 2008-03-05 at 11:54 -0500, gonzalj@purdue.edu wrote:
Hi Nick,
I checked disk space and there are still 59G available, so that should not
be
the problem.
About RAM this system has 3GB.
Any idea of what might be going on?
Thanks a lot,
Javier.
Quoting Nick Schmansky nicks@nmr.mgh.harvard.edu:
Javier,
It should not be necessary to revert to using COR files. How much memory and disk space do you have? We recommend 2GB of ram (and make sure disk space is not empty...freesurfer can fill-up a disk quickly).
Nick
On Wed, 2008-03-05 at 10:28 -0500, gonzalj@purdue.edu wrote:
Hello,
When I run the command "mris_volmask --label_left_white 2
--label_left_ribbon 3
--label_right_white 41 --label_right_ribbon 42 --save_ribbon
--save_distance
DK1" I get the following error:
ERROR: opening pipe gzip -f -c > /home/hammer/a/gonzalj/MirrorNeurons//DK1/mri/lh.dpial.ribbon.mgz,
errno =
12
Cannot allocate memory
mghWrite(/home/hammer/a/gonzalj/MirrorNeurons//DK1/mri/lh.dpial.ribbon.mgz,
-1):
could not open file
I had this error on a previous step and managed to solve it by means
of
using
directories with COR files instead of a single mgz file for input and
output. I
do not see any option in mris_volmask to force it to write each COR
file
independently instead of a single .mgz file. How can I do this so I do
not
run
into a memory problem? Also, any other ideas?
Thanks a lot,
Javier. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Nick,
After a long morning of looking through everything that was running on the computer, I finally made it work after:
(1) Stopping some of the processes that were taking more memory.
(2) Cleaning some stuff on the / filesystem. In fact I think this second point might have been the biggest issue. Although the drive where the data is written has 57G of free space, the / filesystem had only 1.5G free. I do not know if freesurfer might try to temporarily write things in there (such as /tmp), and that migth have been the problem.
The truth is that after making the / filesystem go back to 5G of free space the command mris_volmask run with no problems until the end.
Thanks a lot for your help, I really, really appreciate the quick response you had this morning.
Have a good day,
Javier.
Quoting Nick Schmansky nicks@nmr.mgh.harvard.edu:
Javier,
Does mri_convert output .mgz files? What OS is being used? If mri_convert doesnt produce .mgz files, then I don't know what to suggest.
Nick
On Wed, 2008-03-05 at 12:22 -0500, gonzalj@purdue.edu wrote:
The output of gzip --version is:
gzip 1.3.12 Copyright (C) 2007 Free Software Foundation, Inc. Copyright (C) 1993 Jean-loup Gailly. This is free software. You may redistribute copies of it under the terms
of
the GNU General Public License http://www.gnu.org/licenses/gpl.html. There is NO WARRANTY, to the extent permitted by law.
Written by Jean-loup Gailly.
Javier.
Quoting Nick Schmansky nicks@nmr.mgh.harvard.edu:
Javier,
Which gzip version is being used? (gzip --version)
Nick
On Wed, 2008-03-05 at 11:54 -0500, gonzalj@purdue.edu wrote:
Hi Nick,
I checked disk space and there are still 59G available, so that should
not
be
the problem.
About RAM this system has 3GB.
Any idea of what might be going on?
Thanks a lot,
Javier.
Quoting Nick Schmansky nicks@nmr.mgh.harvard.edu:
Javier,
It should not be necessary to revert to using COR files. How much memory and disk space do you have? We recommend 2GB of ram (and
make
sure disk space is not empty...freesurfer can fill-up a disk
quickly).
Nick
On Wed, 2008-03-05 at 10:28 -0500, gonzalj@purdue.edu wrote:
Hello,
When I run the command "mris_volmask --label_left_white 2
--label_left_ribbon 3
--label_right_white 41 --label_right_ribbon 42 --save_ribbon
--save_distance
DK1" I get the following error:
ERROR: opening pipe gzip -f -c > /home/hammer/a/gonzalj/MirrorNeurons//DK1/mri/lh.dpial.ribbon.mgz,
errno =
12
Cannot allocate memory
mghWrite(/home/hammer/a/gonzalj/MirrorNeurons//DK1/mri/lh.dpial.ribbon.mgz,
-1):
could not open file
I had this error on a previous step and managed to solve it by
means
of
using
directories with COR files instead of a single mgz file for input
and
output. I
do not see any option in mris_volmask to force it to write each
COR
file
independently instead of a single .mgz file. How can I do this so I
do
not
run
into a memory problem? Also, any other ideas?
Thanks a lot,
Javier. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
gonzalj＠purdue.edu -
Nick Schmansky