Hello,

I just wanted to follow up about etiv, if you had the chance to look into if your recon all vs sclimbic also does simithing similar on the subjs i sent?

I am also attaching another graph that depicts the difference between etivs extracted from sclimbic and from recon all.

Thanks for all your help,

Miriam

From: Miriam Taza <miriam.taza@mail.mcgill.ca>
Sent: Wednesday, August 3, 2022 4:59 PM
To: Douglas N. Greve <dgreve@mgh.harvard.edu>
Subject: Re: [Freesurfer] sclimbic sometimes does not detect left basal forebrain

Hello,

Attached are a few subjects, where YA denotes younger adults and OA older adults. I also included the stats file when I run sclimbic for reference. Please let me know if this mode of transfer works.

Thank you,

Miriam

P.S. I also sent a previous email regarding etiv values "etiv value differs if using recon all vs freesurfer dev". Are you able to also see if your sclimbic etiv values differ much from recon all? For example, sub1221084 etiv greatly differs between sclimbic, old recon all, and new recon all.

From: Douglas N. Greve <dgreve@mgh.harvard.edu>
Sent: Friday, July 29, 2022 12:29 PM
To: Miriam Taza <miriam.taza@mail.mcgill.ca>
Subject: Re: [Freesurfer] sclimbic sometimes does not detect left basal forebrain

yes, you can try sending it to me. if they are too big for email, then we have other solutions

On 7/29/2022 12:19 PM, Miriam Taza wrote:

External Email - Use Caution

Hello,

Thank you for your quick response!

I can certainly share a few participants data with you but I would prefer not to share with the entire mailing list if possible. If so, should I attach it to this email?

I could send you more than one if you prefer.

Thank you,

Miriam

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgreve@mgh.harvard.edu>
Sent: Friday, July 29, 2022 12:06 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] sclimbic sometimes does not detect left basal forebrain
Can you send us a sample case?

On 7/28/2022 8:58 PM, Miriam Taza wrote:
Nothing strange about them.

They’re T1w scans 1x1x1mm3

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgreve@mgh.harvard.edu>
Sent: Thursday, July 28, 2022 1:25 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] sclimbic sometimes does not detect left basal forebrain
Have you looked at the input volume to see if there is anything strange about them? What kind of scans are you passing to it? What is the resolution?

On 7/25/2022 9:03 PM, Miriam Taza wrote:
External Email - Use Caution

Hello,

I noticed 20 out of ~240 subjects left basal forebrain volumes were not picked up after running ScLimbic. These are healthy adults and their scans look good. Also, I noticed often when this occurs NAcc is also 0 or other regions.

I am concerned if there is a systematic issue with left volumes ending up smaller than they should relative to right.

Thanks,
Miriam
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