Re: [Freesurfer] Hippocampal segmentation with an additional scan ERROR kvlGEMSMatlab

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Thanks! Did you check whether the T2 and the T1 were correctly registered? You can check out the animated gif under mri/transforms in the subject’s directory. Cheers, /E

-- 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 19:21 To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Hippocampal segmentation with an additional scan ERROR kvlGEMSMatlab

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.ukmailto:e.iglesias@ucl.ac.uk> wrote:

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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Pradeep <tpradeep@gmail.commailto:tpradeep@gmail.com> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Thursday, 4 October 2018 at 19:12 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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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