Re: [Freesurfer] Hippocampal subfields FS6 vs. new hippocampus tool (incl Amygdala) FreeSurfer_dev version

2020-01-24 Thread Iglesias Gonzalez, Juan E. 
Good question! It’s ok if only the hippo is covered.
Cheers,
/E

Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com


From:  on behalf of Rene Seiger 

Reply-To: Freesurfer support list 
Date: Friday, 24 January 2020 at 12:15
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: Re: [Freesurfer] Hippocampal subfields FS6 vs. new hippocampus tool 
(incl Amygdala) FreeSurfer_dev version


External Email - Use Caution

Dear Juan,

Thank you very much for you answer! However, I ran into another issue using the 
new tool: It is stated:  'Using the additional scan in isolation is advised 
when it is of higher resolution than the T1 while covering the whole hippocampi 
and amygdalae'. Can I still use this processing mode, when my high-resolution 
scans only have the hippocampi covered, as I am not interested in the amygdala 
in the first place? Or is it mandatory to have both structures fully covered 
within the additional scan when I want to run it in isolation?
Thank you very much,
René



<http://www.meduniwien.ac.at/neuroimaging/>
<http://www.meduniwien.ac.at/neuroimaging/>
Am 23.01.2020 um 18:09 schrieb Iglesias Gonzalez, Juan E.:
Hi Rene,
The atlases are slightly different so the outputs will be a bit different. But 
the segmentations will indeed be comparable.
Cheers,
/Eugenio

Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com


From: 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Rene Seiger 
<mailto:rene.sei...@meduniwien.ac.at>
Reply-To: Freesurfer support list 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Date: Thursday, 23 January 2020 at 07:48
To: "freesurfer@nmr.mgh.harvard.edu"<mailto:freesurfer@nmr.mgh.harvard.edu> 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Hippocampal subfields FS6 vs. new hippocampus tool (incl 
Amygdala) FreeSurfer_dev version


External Email - Use Caution

Dear all,

I recently saw that the page of the hippocampal module for FS6 
(https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields) seems to be 
obsolete and it looks as if this module will be replaced by a newer version in 
the near future (now dev version, 
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala).

However, I am not entirely sure how those two modules differ in terms of 
hippocampal subfield segmentation, when the "FS60" parcellation scheme is used 
in the new module. It is stated that 'it mimics the FreeSurfer 6.0 hippocampal 
module', but is the output 1:1 comparable?
Thank you very much and kind regards,
René
--

Dr. René Seiger
Research Associate

Medical University of Vienna
Department of Psychiatry and Psychotherapy
Division of General Psychiatry
NEUROIMAGING LABS (NIL) - PET, MRI, EEG, TMS & Chemical Lab

Waehringer Guertel 18-20, A-1090 Vienna
Phone +43 (0) 1 40400-38250
rene.sei...@meduniwien.ac.at
<mailto:rene.sei...@meduniwien.ac.at>http://www.meduniwien.ac.at/neuroimaging/

<http://www.meduniwien.ac.at/neuroimaging/>



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Re: [Freesurfer] Hippocampal subfields FS6 vs. new hippocampus tool (incl Amygdala) FreeSurfer_dev version

2020-01-24 Thread Rene Seiger 
   External Email - Use Caution


Dear Juan,

Thank you very much for you answer! However, I ran into another issue 
using the new tool: It is stated:  'Using the additional scan in 
isolation is advised when it is of higher resolution than the T1 while 
covering the whole hippocampi and amygdalae'. Can I still use this 
processing mode, when my high-resolution scans only have the hippocampi 
covered, as I am not interested in the amygdala in the first place? Or 
is it mandatory to have both structures fully covered within the 
additional scan when I want to run it in isolation?


Thank you very much,
René



<http://www.meduniwien.ac.at/neuroimaging/>
<http://www.meduniwien.ac.at/neuroimaging/>
Am 23.01.2020 um 18:09 schrieb Iglesias Gonzalez, Juan E.:


Hi Rene,

The atlases are slightly different so the outputs will be a bit 
different. But the segmentations will indeed be comparable.


Cheers,

/Eugenio

Juan Eugenio Iglesias

Senior research fellow

CMIC (UCL), MGH (HMS) and CSAIL (MIT)

http://www.jeiglesias.com

*From: * on behalf of Rene 
Seiger 

*Reply-To: *Freesurfer support list 
*Date: *Thursday, 23 January 2020 at 07:48
*To: *"freesurfer@nmr.mgh.harvard.edu" 
*Subject: *[Freesurfer] Hippocampal subfields FS6 vs. new hippocampus 
tool (incl Amygdala) FreeSurfer_dev version


*External Email - Use Caution *

Dear all,

I recently saw that the page of the hippocampal module for FS6 
(https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields) seems 
to be obsolete and it looks as if this module will be replaced by a 
newer version in the near future (now dev version, 
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala).


However, I am not entirely sure how those two modules differ in terms 
of hippocampal subfield segmentation, when the "FS60" parcellation 
scheme is used in the new module. It is stated that 'it mimics the 
FreeSurfer 6.0 hippocampal module', but is the output 1:1 comparable?


Thank you very much and kind regards,
René

--

*Dr. René Seiger*
Research Associate

*Medical University of Vienna*
Department of Psychiatry and Psychotherapy
Division of General Psychiatry
NEUROIMAGING LABS (NIL) - PET, MRI, EEG, TMS & Chemical Lab

Waehringer Guertel 18-20, A-1090 Vienna
Phone +43 (0) 1 40400-38250
rene.sei...@meduniwien.ac.at
<mailto:rene.sei...@meduniwien.ac.at>http://www.meduniwien.ac.at/neuroimaging/ 



<http://www.meduniwien.ac.at/neuroimaging/>


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Re: [Freesurfer] Hippocampal subfields FS6 vs. new hippocampus tool (incl Amygdala) FreeSurfer_dev version

2020-01-23 Thread Iglesias Gonzalez, Juan E. 
Hi Rene,
The atlases are slightly different so the outputs will be a bit different. But 
the segmentations will indeed be comparable.
Cheers,
/Eugenio

Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com


From:  on behalf of Rene Seiger 

Reply-To: Freesurfer support list 
Date: Thursday, 23 January 2020 at 07:48
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] Hippocampal subfields FS6 vs. new hippocampus tool (incl 
Amygdala) FreeSurfer_dev version


External Email - Use Caution

Dear all,

I recently saw that the page of the hippocampal module for FS6 
(https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields) seems to be 
obsolete and it looks as if this module will be replaced by a newer version in 
the near future (now dev version, 
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala).

However, I am not entirely sure how those two modules differ in terms of 
hippocampal subfield segmentation, when the "FS60" parcellation scheme is used 
in the new module. It is stated that 'it mimics the FreeSurfer 6.0 hippocampal 
module', but is the output 1:1 comparable?
Thank you very much and kind regards,
René
--

Dr. René Seiger
Research Associate

Medical University of Vienna
Department of Psychiatry and Psychotherapy
Division of General Psychiatry
NEUROIMAGING LABS (NIL) - PET, MRI, EEG, TMS & Chemical Lab

Waehringer Guertel 18-20, A-1090 Vienna
Phone +43 (0) 1 40400-38250
rene.sei...@meduniwien.ac.at
<mailto:rene.sei...@meduniwien.ac.at>http://www.meduniwien.ac.at/neuroimaging/

<http://www.meduniwien.ac.at/neuroimaging/>
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[Freesurfer] Hippocampal subfields FS6 vs. new hippocampus tool (incl Amygdala) FreeSurfer_dev version

2020-01-23 Thread Rene Seiger 
   External Email - Use Caution


Dear all,

I recently saw that the page of the hippocampal module for FS6 
(https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields) seems 
to be obsolete and it looks as if this module will be replaced by a 
newer version in the near future (now dev version, 
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala).


However, I am not entirely sure how those two modules differ in terms of 
hippocampal subfield segmentation, when the "FS60" parcellation scheme 
is used in the new module. It is stated that 'it mimics the FreeSurfer 
6.0 hippocampal module', but is the output 1:1 comparable?


Thank you very much and kind regards,
René
--

*Dr. René Seiger*
Research Associate

*Medical University of Vienna*
Department of Psychiatry and Psychotherapy
Division of General Psychiatry
NEUROIMAGING LABS (NIL) - PET, MRI, EEG, TMS & Chemical Lab

Waehringer Guertel 18-20, A-1090 Vienna
Phone +43 (0) 1 40400-38250
rene.sei...@meduniwien.ac.at
http://www.meduniwien.ac.at/neuroimaging/ 




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