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-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@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-bounces@nmr.mgh.harvard.edu> on behalf of "Mennecke, Angelika" <Angelika.Mennecke@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