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OK yes this is a problem with the main recon-all stream. It’d have been a
miracle for the subfield module to recover from that…
At this point, I’ll defer to Doug / Bruce.
Cheers,
/E
--
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com
From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of "Mennecke,
Angelika" <angelika.menne...@uk-erlangen.de>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Monday, 17 June 2019 at 10:11
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] hippocampal subfields error
External Email - Use Caution
Dear Eugenio,
attached you’ll find the picture. Looks as though the left hippocampus has
erroneously been attributed to gray matter.
Cheers, Angelika
Von: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Iglesias
Gonzalez, Eugenio
Gesendet: Montag, 17. Juni 2019 15:49
An: Freesurfer support list
Betreff: Re: [Freesurfer] hippocampal subfields error
External Email - Use Caution
Dear Angelika,
Can you please send us a screenshot of the inaccurate T1 segmentation?
Cheers,
/Eugenio
--
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com
From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of "Mennecke,
Angelika" <angelika.menne...@uk-erlangen.de>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Monday, 17 June 2019 at 06:36
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] hippocampal subfields error
External Email - Use Caution
Hi all,
I’m doing hippocampal subfields analysis with freesurfer 6.0 with T1 and high
resolution T2 data from a 7T MRT. With at least one of my datasets Matlab
throws an error during the hippocampal-subfields-T2 –pipeline:
Making Unknown map to reduced label 14
Computing hyperparameters for estimation of Gaussians of T2 data
Error using |
Inputs must have the same size.
Error in segmentSubjectT2_autoEstimateAlveusML (line 1064)
With other patients, the pipeline on the T2 images is correctly working without
errors. I’m wondering what is causing this error and whether there is something
I can do to avoid it?
As far as I can see, the only difference between the “error” dataset and the
others is that hippocampal subfields-T1 is also not calculated correctly. It
finishes without errors, but the final result does not cover the hippocampus
correctly (probably due to a T1-hypointense cyst in the hippocampus of that
patient).
Best regards,
Angelika
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