I'm not sure but I have a guess. EAch stage of the unet has an intensity
normalization step where the intensity of all voxels are spread
uniformly over a range. I suspect that the bright, meaningless voxels
are causing the meaningful voxels to be forced into too small of a range
causing information loss.
On 8/31/2022 11:19 AM, Miriam Taza wrote:
External Email - Use Caution
thank you!
One last question hopefully on this matter. I dont fully understand
still why the percentile flag would affect the subcortical regions?
the bias field was only in the front and back of the brain.
Thanks,
Miriam
------------------------------------------------------------------------
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve
<dgr...@mgh.harvard.edu>
*Sent:* Sunday, August 28, 2022 4:13 PM
*To:* freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
*Subject:* Re: [Freesurfer] sclimbic sometimes does not detect left
basal forebrain
On 8/11/2022 6:02 PM, Miriam Taza wrote:
External Email - Use Caution
Hi again,
I have a few questions regarding this.
indeed it does appear that there is a bias field in all of these
scans, but this is not specific to those that fail sclimbic.
1. 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).
I have no idea. That's the problem with the machine learning stuff, it
just gives you an answer without a reason.
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....
The --percentile 99.9 tells it to sort all the voxels by intensity.
One of those voxels will rank the 99.9% in intensity. All voxels that
are brighter than this intensity are then set to this intensity
("clipping"). This represents more closely how ScLimbic was trained. I
will make --percentile 99.9 the default on the next release.
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.
*
*This confirms my suspicions above (ie, the training). The "recon"
method will most closely track the training (and the results from the
paper).*
Thank you very much!
Miriam
------------------------------------------------------------------------
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu>
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Miriam
Taza <miriam.t...@mail.mcgill.ca> <mailto:miriam.t...@mail.mcgill.ca>
*Sent:* Wednesday, August 10, 2022 1:26 PM
*To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
<mailto:freesurfer@nmr.mgh.harvard.edu>
*Subject:* Re: [Freesurfer] sclimbic sometimes does not detect left
basal forebrain
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-boun...@nmr.mgh.harvard.edu
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu>
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas
N. Greve <dgr...@mgh.harvard.edu> <mailto:dgr...@mgh.harvard.edu>
*Sent:* Tuesday, August 9, 2022 10:34 PM
*To:* freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>
<freesurfer@nmr.mgh.harvard.edu> <mailto: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-boun...@nmr.mgh.harvard.edu
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu>
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas
N. Greve <dgr...@mgh.harvard.edu> <mailto:dgr...@mgh.harvard.edu>
*Sent:* Thursday, July 28, 2022 1:25 PM
*To:* freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>
<freesurfer@nmr.mgh.harvard.edu> <mailto: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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