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

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