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
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
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): srishtig@email.unc.edu skype: srishti.goel12
On Thu, Apr 5, 2018 at 12:16 PM, Bruce Fischl fischl@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 256voxel 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: 0.00degrees
nframes: 1 PhEncDir: UNKNOWN FieldStrength: 0.000000ras 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_Te st/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 1.0000voxel-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 1.0000Is 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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): srishtig@email.unc.edu skype: srishti.goel12
On Thu, Apr 5, 2018 at 12:16 PM, Bruce Fischl fischl@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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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 srishtig@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): srishtig@email.unc.edu skype: srishti.goel12
On Thu, Apr 5, 2018 at 12:24 PM, Bruce Fischl fischl@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 freeshared 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): srishtig@email.unc.edu skype: srishti.goel12
On Thu, Apr 5, 2018 at 12:16 PM, Bruce Fischl <fischl@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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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 srishtig@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): srishtig@email.unc.edu skype: srishti.goel12
On Thu, Apr 5, 2018 at 12:24 PM, Bruce Fischl fischl@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): srishtig@email.unc.edu skype: srishti.goel12 On Thu, Apr 5, 2018 at 12:16 PM, Bruce Fischl <fischl@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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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): srishtig@email.unc.edu skype: srishti.goel12
On Thu, Apr 5, 2018 at 12:31 PM, Bruce Fischl fischl@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 srishtig@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): srishtig@email.unc.edu skype: srishti.goel12
On Thu, Apr 5, 2018 at 12:24 PM, Bruce Fischl fischl@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 thememory usage from recon-all.log
total used free shared buff/cache available Mem: 263726968 34330048 152102696 1294477294224 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): srishtig@email.unc.edu skype: srishti.goel12 On Thu, Apr 5, 2018 at 12:16 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Srishti
are you sure that your machine didn't just run out ofmemory? 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 errorwhile 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 checkmri_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 0.0000127.0000
0.0000 0.0000 1.0000-90.5000
0.0000 -1.0000 0.0000132.7185
0.0000 0.0000 0.00001.0000
voxel-to-ras determinant -1 ras to voxel transform: -1.0000 -0.0000 -0.0000127.0000
-0.0000 -0.0000 -1.0000132.7185
-0.0000 1.0000 -0.000090.5000
-0.0000 -0.0000 -0.00001.0000
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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for theperson to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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): srishtig@email.unc.edu skype: srishti.goel12
On Thu, Apr 5, 2018 at 12:31 PM, Bruce Fischl fischl@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 srishtig@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): srishtig@email.unc.edu skype: srishti.goel12 On Thu, Apr 5, 2018 at 12:24 PM, Bruce Fischl <fischl@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): srishtig@email.unc.edu skype: srishti.goel12 On Thu, Apr 5, 2018 at 12:16 PM, Bruce Fischl <fischl@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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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): srishtig@email.unc.edu skype: srishti.goel12
On Thu, Apr 5, 2018 at 12:43 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu 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): srishtig@email.unc.edu skype: srishti.goel12
On Thu, Apr 5, 2018 at 12:31 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Srishti
if you look in the subject's scripts dir there should be a filenamed "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 thecommand line directly? I use the following command:
sbatch --mem 2200 -t 6-00:00 --mail-type END --mail-usersrishtig@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 submissioncommand 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): srishtig@email.unc.edu skype: srishti.goel12 On Thu, Apr 5, 2018 at 12:24 PM, Bruce Fischl <fischl@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 usedfree 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): srishtig@email.unc.edu skype: srishti.goel12 On Thu, Apr 5, 2018 at 12:16 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Srishti
are you sure that your machine didn't justrun 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 structuralbrains 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, therewas 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: 0.00msec, 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 0.00000.0000 127.0000
0.0000 0.00001.0000 -90.5000
0.0000 -1.00000.0000 132.7185
0.0000 0.00000.0000 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 resolvethis 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended onlyfor the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for theperson to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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): srishtig@email.unc.edu skype: srishti.goel12
On Thu, Apr 5, 2018 at 12:43 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu 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): srishtig@email.unc.edu skype: srishti.goel12 On Thu, Apr 5, 2018 at 12:31 PM, Bruce Fischl <fischl@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 srishtig@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): srishtig@email.unc.edu skype: srishti.goel12 On Thu, Apr 5, 2018 at 12:24 PM, Bruce Fischl <fischl@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): srishtig@email.unc.edu skype: srishti.goel12 On Thu, Apr 5, 2018 at 12:16 PM, Bruce Fischl <fischl@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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
srishti goel