External Email - Use Caution
Dear Freesurfer developers, After we run recon-all in a subject we noticed some mistakes, so we added manually some control points in a point set we named control.dat. Then we tried to run autorecon, with the command: recon-all -autorecon2-cp -autorecon3 -subjid Sub42 but we stumbled upon the following error message:
using control points from file /project/data/scans/subject/Sub42/tmp/control.dat...
assuming input volume is MGH (Van der Kouwe) MP-RAGE
using segmentation for initial intensity normalization
using MR volume brainmask.mgz to mask input volume...
reading from norm.mgz...
Reading aseg aseg.presurf.mgz
normalizing image...
Reading 133 control points...
only using 133 control points from file, mean 69.1, scaling by 1.59...
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
processing with aseg
removing outliers in the aseg WM...
580 control points removed
Building bias image
building Voronoi diagram...
performing soap bubble smoothing, sigma = 0...
Smoothing with sigma 8
Applying bias correction
HISTOalloc(-2147483648): could not allocate histogram
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Iterating 2 times
---------------------------------
3d normalization pass 1 of 2
white matter peak found at 110
Cannot allocate memory
Linux hpc137 2.6.32-696.16.1.el6.x86_64 #1 SMP Wed Nov 15 16:51:15 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s Sub42 exited with ERRORS
What do you think is the problem?
Thank you in advance!
Best regards,
Eleni
Can you upload the subject? Follow the instructions below
From the linux command line, Create the file you want to upload, eg, cd $SUBJECTS_DIR tar cvfz subject.tar.gz ./subject Now log into our anonymous FTP site: ftp surfer.nmr.mgh.harvard.edu It will ask you for a user name: use "anonymous" (no quotes) It will ask you for a password: use "anonymous" (no quotes) cd transfer/incoming binary put subject.tar.gz Send an email that the file has been and the name of the file.
On 9/18/2020 12:31 PM, Eleni Nikalexi wrote:
External Email - Use Caution
Dear Freesurfer developers,
After we run recon-all in a subject we noticed some mistakes, so we added manually some control points in a point set we named control.dat. Then we tried to run autorecon, with the command: recon-all -autorecon2-cp -autorecon3 -subjid Sub42
but we stumbled upon the following error message:
using control points from file /project/data/scans/subject/Sub42/tmp/control.dat...
assuming input volume is MGH (Van der Kouwe) MP-RAGE
using segmentation for initial intensity normalization
using MR volume brainmask.mgz to mask input volume...
reading from norm.mgz...
Reading aseg aseg.presurf.mgz
normalizing image...
Reading 133 control points...
only using 133 control points from file, mean 69.1, scaling by 1.59...
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
processing with aseg
removing outliers in the aseg WM...
580 control points removed
Building bias image
building Voronoi diagram...
performing soap bubble smoothing, sigma = 0...
Smoothing with sigma 8
Applying bias correction
HISTOalloc(-2147483648): could not allocate histogram
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Iterating 2 times
3d normalization pass 1 of 2
white matter peak found at 110
Cannot allocate memory
Linux hpc137 2.6.32-696.16.1.el6.x86_64 #1 SMP Wed Nov 15 16:51:15 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s Sub42 exited with ERRORS
What do you think is the problem?
Thank you in advance!
Best regards,
Eleni
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Douglas N. Greve -
Eleni Nikalexi