-- 

Juan Eugenio Iglesias

ERC Senior Research Fellow

Centre for Medical Image Computing (CMIC)

University College London

Research staff

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

Research Affiliate

Computer Science and Artificial Intelligence Laboratory (CSAIL)

Massachusetts Institute of Technology

Lecturer on Radiology

Harvard Medical School

http://www.jeiglesias.com 

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Yixin Ma <yixinma9@gmail.com>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Tuesday, 22 January 2019 at 10:09
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Hippocampus subfield division error

Hi Dr.

Iglesias

Hi,

 

The hippocampus subfields division problem happens on more than one subjects (~10). However, I have successfully run it on one subject (which is a little earlier in time, before I failed to run recent 10 subjects). Thank you for your help. 

 

Best regards,

 

Yixin

 

---------- Forwarded message ---------
From: Yixin Ma <yixinma9@gmail.com>
Date: Fri, Jan 18, 2019 at 11:04 AM
Subject: Hippocampus subfield division error
To: <freesurfer@nmr.mgh.harvard.edu>

 

Hi FreeSurfer experts,

 

I'm writing to ask about the hippocampus subfields division in FreeSurfer 6.0.

 

I got an error message as attached, could you please help me with which part might have gone wrong? This subject's other recon-all worked but not for hippocampus subfields division.

 

Thank you for your help. 

 

Best regards,

 

Yixin

 

[ > In segmentSubjectT1_autoEstimateAlveusML at 325]  

Reading contexts of file /usr/local/packages/freesurfer_v6.0.0/average/HippoSF/atlas/compressionLookupTable.txt

--------------

Making Lateral-nucleus map to reduced label 1

Making Paralaminar-nucleus map to reduced label 1

Making Basal-nucleus map to reduced label 1

Making Accessory-Basal-nucleus map to reduced label 1

Making Corticoamygdaloid-transitio map to reduced label 1

Making Central-nucleus map to reduced label 1

Making Cortical-nucleus map to reduced label 1

Making Medial-nucleus map to reduced label 1

Making Anterior-amygdaloid-area-AAA map to reduced label 1

--------------

Making alveus map to reduced label 2

Making Hippocampal_tail map to reduced label 2

Making HATA map to reduced label 2

Making fimbria map to reduced label 2

Making parasubiculum map to reduced label 2

Making hippocampal-fissure map to reduced label 2

--------------

Making Left-Cerebral-Cortex map to reduced label 3

--------------

Making Left-Cerebral-White-Matter map to reduced label 4

--------------

Making Left-Lateral-Ventricle map to reduced label 5

--------------

Making Left-choroid-plexus map to reduced label 6

--------------

Making Unknown map to reduced label 7

--------------

Making Left-VentralDC map to reduced label 8

--------------

Making Left-Putamen map to reduced label 9

--------------

Making Left-Pallidum map to reduced label 10

--------------

Making Left-Thalamus-Proper map to reduced label 11

--------------

Making Left-Accumbens-area map to reduced label 12

--------------

Making Left-Caudate map to reduced label 13

Error using segmentSubjectT1_autoEstimateAlveusML (line 348)

The vector of prior probabilities in the mesh nodes must always sum to one over all classes