why do you think it is consistently only the left side that fails? My question here is if whether it is mainly the left due to the way sclimbic does its magic or if this might be due to the actual data (i,e smaller left volumes might have an impact).

2. I would really appreciate if someone could explain what --percentile 99.9 is doing a bit more as my results differ a lot depending if this flag is used or not.

Im asking because Im not sure what is the best input to use for sclimbic anymore....

I decided to look at differences(correlation) of volume (.stats) between sclimbic or sclimbic with --percentile 99.9 ran on T1s or on recon all results (I wanted to make confirm the results using recon all subj vs t1s with the percentile flag are similar given that recon all does correct for bias field). below are the correlation and means. this was on subsample (n=180) and I only looked at one ROI.

	left BF	right BF
sclimbic x sclimbic99	0.48	0.62
sclimbic x recon99	0.30	0.55
sclimbic x recon	0.30	0.55
recon99 x recon	0.99	0.99
recon99 x sclimbic99	0.91	0.95
recon x sclimbic99	0.92	0.95

	avg left BF	avg BF mean
sclimbic	198.77	253.96
sclimbic99	297.99	328.93
recon	312.12	340.44
recon99	315.80	343.92

(recon = sclimbic ran on recon all outputs; recon99 = sclimbic --percentile 99 ran on recon outputs; sclimbic=ran sclimbic on t1s; sclimbic99=with flag ran on t1s)

3.so the most important question is what would you judge to provide the "most accurate" result to be used in subsequent group analysis. recon99, recon, sclimbic, or sclimbic99.

Thank you very much!

Miriam

External Email - Use Caution

but this(bright at back and nose) also seems to be the case with participants that sclimbic did work on..

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgreve@mgh.harvard.edu>
Sent: Tuesday, August 9, 2022 10:34 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] sclimbic sometimes does not detect left basal forebrain

There was something a little strange about the cases that were failing -- there were very bright values at the back of the head and around the nose. This probably messes up the normalization in the unet. I ran it with --percentile 99.9 (this eliminates the extreme voxels) and the results looked ok after that.

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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