HI Malav, did you create the subcortical mass? Have you separated the
hemispheres?
On 4/18/2022 4:48 PM, Malav Shah wrote:
External Email - Use Caution
Hi Dr. Greve,
I send a gentle reminder, in case the previous mail skipped your
attention.
with regards,
Malav
------------------------------------------------------------------------
*From: *"Malav Shah" <malav.s...@bccn-berlin.de>
*To: *"Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
*Sent: *Tuesday, April 12, 2022 3:08:50 PM
*Subject: *Re: [Freesurfer] recontruction of an elephant brain
Hi Douglas,
thank you so much for your suggestions.
Your understanding of my task is very precise, and I would love to
move in the direction you recommend. I would appreciate a bit more
detailed guidance.
Would you have a little bit of time to spare for me in those regards?
Looking foward,
Malav Shah
------------------------------------------------------------------------
*From: *"Douglas N. Greve" <dgr...@mgh.harvard.edu>
*To: *"freesurfer" <freesurfer@nmr.mgh.harvard.edu>
*Sent: *Saturday, April 9, 2022 10:18:18 PM
*Subject: *Re: [Freesurfer] recontruction of an elephant brain
Lot's of people have adapted FS to non-human brains, just google it.
For surface analysis, you need to get the "subcortical mass" -- the
equivalent to the filled.mgz. This is the cerebral white matter +
subcort gray structures. Once you have that, you might be able to run
mris_place_surfaces. I'd have to walk you through the options to use
or not.
On 4/8/2022 6:01 AM, Malav Shah wrote:
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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." <lzol...@mgh.harvard.edu>
<mailto:lzol...@mgh.harvard.edu>
*To: *"freesurfer" <freesurfer@nmr.mgh.harvard.edu>
<mailto: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:
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As far as I know elephant brain images have not yet been
processed. Good luck, Lilla
------------------------------------------------------------------------
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu>
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Malav
Shah <malav.s...@bccn-berlin.de> <mailto:malav.s...@bccn-berlin.de>
*Sent:* Wednesday, April 6, 2022 1:10 PM
*To:* freesurfer@nmr.mgh.harvard.edu
<freesurfer@nmr.mgh.harvard.edu>
<mailto: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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