External Email - Use Caution
I have tried this for two subjects and got the same error.
Thanks, Pradeep
On Thu, Oct 4, 2018 at 11:14 AM Iglesias Gonzalez, Eugenio < e.iglesias@ucl.ac.uk> wrote:
External Email - Use CautionDear Pradeep,
Did you get this error on several subjects, or only one?
Cheers,
/Eugenio
--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
*From: *freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Pradeep < tpradeep@gmail.com> *Reply-To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Date: *Thursday, 4 October 2018 at 19:12 *To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject: *[Freesurfer] Hippocampal segmentation with an additional scan ERROR kvlGEMSMatlab
External Email - Use Caution *Hello,
I am trying to run the hippocampal segmentation with an additional Hi-res scan using the following command
recon-all -s <subject_name> -hippocampal-subfields-T2 <file name of additional scan> <analysisID>
and got the following error
Error using kvlGEMSMatlab
/autofs/cluster/koen/eugenio/InsightToolkit-4.9.1/Modules/Core/Common/include/itkImageConstIterator.h:211:
itk::ERROR: Region ImageRegion (0x7f67011c5dd0)
Dimension: 3
Index: [0, 845, 0]
Size: [105, 18446744073709550952, 20]
is outside of buffered region ImageRegion (0x7f6573ca8bb8)
Dimension: 3
Index: [0, 0, 0]
Size: [526, 181, 526]
Error in kvlReadCroppedImage (line 11)
Error in segmentSubjectT2_autoEstimateAlveusML (line 838)
Started at Thu Oct 4 09:35:38 MST 2018
Ended at Thu Oct 4 09:57:35 MST 2018
#@#%# recon-all-run-time-hours 0.366
recon-all -s subject_id finished without error at Thu Oct 4 09:57:36 MST 2018
done
I came across a similar error in the forums and using the most recent version seem to have worked for some, but it did not help in my case.
Freesurfer version I am using
Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a
Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a
with matlab run time from 2012b as suggested
I have also tried to use 2014b runtime which exited right away.
Thank you for your help,
Pradeep
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