Use the same command for every case
On 8/10/2022 1:15 PM, Miriam Taza wrote:
External Email - Use Caution
oh interesting, do you recommend rerunning all with -percentile 99.9?
Would it make much difference to the results? or would it be ok to
just run those with missing left?
------------------------------------------------------------------------
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve
<dgr...@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-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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