External Email - Use Caution        

Dear 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

http://www.jeiglesias.com

http://cmictig.cs.ucl.ac.uk/

 

 

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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