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_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 1.0000
>>
>>
>> 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.
