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Hi Lilla,
Thank you so much for your feedback.
I completely understand the tool's bias for human brains. As you said, the elephant brain images are not well understood so far. We aim to take initial steps in that direction, starting with small goals like WM-GM seperation, cortical thickness measurements, and surface visualisation with flattening. Do you think it can be achieved with FreeSurfer's volume-based analysis pipeline? We would be more than happy to collaborate on that.
Looking forward to hearing from you :) Thanks and regards, Malav Shah
From: "Zollei, Lilla,Ph.D." LZOLLEI@MGH.HARVARD.EDU To: "freesurfer" freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, April 6, 2022 8:29:33 PM Subject: Re: [Freesurfer] recontruction of an elephant brain
Hi Malav,
Freesurfer is guided by an atlas that was built from human adult brain images. In the past though, we did have collaborators who have tried some modified versons of the pipeline to work on non-human data. Here are some pointers:
[ https://secure-web.cisco.com/1149bxkRGOm5AzvVYmA-Bxc160t7HU-wHF-xUFdBZaQ-CBD... | https://secure-web.cisco.com/1149bxkRGOm5AzvVYmA-Bxc160t7HU-wHF-xUFdBZaQ-CBD... ] [ https://secure-web.cisco.com/1hWAtvKnqtTh7X5HFZdRhQKvG5qfkbftxeOlgW8K8ZQVAWK... | https://secure-web.cisco.com/1hWAtvKnqtTh7X5HFZdRhQKvG5qfkbftxeOlgW8K8ZQVAWK... ]
As far as I know elephant brain images have not yet been processed. G ood luck, Lilla
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Malav Shah malav.shah@bccn-berlin.de Sent: Wednesday, April 6, 2022 1:10 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] recontruction of an elephant brain
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hi, I am trying to reconstruct elephant brain MRI. I am wondering if FreeSurfer can manage this, or does the recon-all command has an inherent bias for human data. Does anyone have an experience using FreeSurfer with a non-human mammal for such purposes?
I have some hopes with this idea, because I am not trying to achieve parcellation or segmentation. Rather, we want to separate White matter from grey Matter, and then probe into various surface measurements across cortical regions. So as per my understanding, all I am expecting from FreeSurfer, is WM-GM segregation, and later (if possible) cortical surface flattening, and DTI.
All words of advice are welcome. Thanks :)
Malav Shah PhD candidate, Michael Brecht Lab, Humboldt University zu Berlin. (+49) 163-216-9391
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