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
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-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
External Email - Use Caution
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-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 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-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
hmmm, that is strange. Can you tar and gzip the entire subject dir then upload it to our ftp site?
On Mon, 17 Jun 2019, Iglesias Gonzalez, Eugenio wrote:
External Email - Use Caution
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)
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 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-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)
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
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Iglesias Gonzalez, Eugenio -
Mennecke, Angelika