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Hi Dr. 00246.zip https://drive.google.com/file/d/17ZePu_X5BqpJNT2u5yEUhNHh8jH1dSIL/view?usp=drive_web Iglesias
I have the problem of hippocampus subfield division not working. You mentioned that I can upload one of the subjects as an example. I'm not sure what kinds of file do you want, so I uploaded the folder of the FreeSurfer reconstruction results, as attached. Thank you again for your help.
Best regards,
Yixin
On Fri, Jan 18, 2019 at 12:28 PM Yixin Ma yixinma9@gmail.com wrote:
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