[Freesurfer] Vertex-wise analysis using ComBat

[Rene Seiger]

   External Email - Use Caution


Dear FreeSurfer community!

We collected structural data from different scanners and we want to 
conduct a surface-based (vertex-wise) analysis in FreeSurfer using 
predefined regions of interest. The model is quite simple, as we just 
want to correlate a specific (e.g. behavioral) measurement from all 
subjects (one group) with the thickness on the surface in specific ROIs. 
To account for the different scanner types, we are planning to use 
ComBat to account for this effect. However, we are not quite sure how 
and at which stage we could implement ComBat using the standard 
FreeSurfer FSGD file approach. Any help would be highly appreciated, 
Thanks!
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Re: [Freesurfer] Hippocampal subfields FS6 vs. new hippocampus tool (incl Amygdala) FreeSurfer_dev version

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

[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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