Re: [Freesurfer] freeview command line options

[Tim Schäfer]

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Dear Eli,

could you add the command line you used and the FreeSurfer version (e.g., 
output of `cat ${FREESURFER_HOME}/VERSION`)?

Thanks,

Tim

> On September 20, 2019 at 10:14 PM "Rockers, Elijah D." 
>  wrote:
> 
> 
> External Email - Use Caution
> 
> Hello, it's possible I found a bug in freeview:
> 
> I'm using the overlay_color option with freeview. Specifically I am trying to 
> use both the "truncate" and "inverse" options in a command line call to 
> freeview for a pipeline I am building. The documentation says that I can 
> apply more than one, delimited by commas  however I have found that if I 
> attempt to use both truncate and inverse, it seems to be only applying 
> whichever one appears last on the list.
> 
> In an interactive instance of freeview, doing everything manually, I have no 
> problems. Just seems to be an issue with the command line call. Any 
> suggestions on how I might proceed in this case?
> 
> -Eli
> 
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[Freesurfer] help! Hippocampal subfield segmentation with FS development version

[Liwen Zhang]

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Hello freesurfer experts,
I previously applied hippocampal subfield segmentation using FS v.6.0. I am now 
trying to devide subfields into head/body where applicable using FS development 
version (latest version). However, I encountered the following 
problems/quesetions:
1) X represents certain subfield (volume)X_head + X_body (from FS dev) ~= X 
(from FS v.6.0)
What possibly causes this volume discrepancy between FS dev and FS v.6.0? Is 
the head/body segmentation template in FS dev based on the same ex-vivo 
template as used in FS v.6.0?
2) Related to 1), subfield volume as obtained from FS v.6.0 generally larger 
than that from FS dev (not for all subfields though)
I processed T1 images with FS v.6.0 and then applied hippocampal segmentation 
with both FS v.6.0 and FS dev. 
Any suggestions/comments would be greatly appreicated! 
Thank you for your time and help in advance!
Best, Liwen

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