from recon all command or from sclimbic.
Thanks,
Miriam
From: Miriam Taza
Sent: Thursday, August 11, 2022 6:01 PM
To: Greve, Douglas N.,Ph.D.
Subject: Re: [Freesurfer] sclimbic sometimes does not detect left basal
forebrain
Hello,
I just wanted to follow up about
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
Sent: Sunday, August 28, 2022 4:13 PM
To: 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
be used in subsequent group analysis. recon99, recon,
sclimbic, or sclimbic99.
Thank you very much!
Miriam
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Miriam Taza
Sent: Wednesday, August 10, 2022 1:26 PM
To: Freesurfer support list
Subject: Re: [
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Hi,
I recently installed the new FS on my mac. I renamed my old "freesurfer" folder
as instructed on the wiki.
However now freeview crashes. it opens but when i try to load volume it
crashes. Below you will find the report. (this happens if I use eith
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
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
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:
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Hello,
I noticed 20 out of ~240 subjects
mp file in
$SUBJECTS_DIR/subject/scripts (should be in the recon-all.log too)
On 7/28/2022 1:41 PM, Miriam Taza wrote:
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is it not these two lines?
# cvs_version $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $
# cvs_version dev
if not, for the new recon-all I
freesurfer
dev
What version of FS are you using for recon-all?
On 7/25/2022 9:45 PM, Miriam Taza wrote:
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I reran sclimbic and I get the same result as the first time I ran sclimbic.
I also reran recon all on one subject. The etiv now differs from the original
recon
why this is happening with etiv nor what value to
>accept.
Please let me know if there is something else I can do or if you need more info.
Miriam
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Miriam Taza
Sent: Monday, July 25, 2022 2:45 PM
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
-vol
--surf-ctx-vol --totalgray --euler --ctab
/usr/local/freesurfer/7.2.0/ASegStatsLUT.txt --subject subject
Check the eTIV in redo.aseg.stats against that in aseg.stats, then re-run
mri_sclimbic_seg to see if the results agree.
On 7/24/2022 6:19 PM, Miriam Taza wrote:
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Hello,
I am getting different etiv values when running recon(orange) all VS
mri_sclimbic_seg (blue). My analysis uses limbic volumes extracted from the dev
version but I am not sure if I should just use the etiv from recon all, given
the data is tig
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Hello,
I am trying to run mri_sclimbic_seg command using dev version of freesurfer on
my macbook pro m1 max (monterey version 12.2.1) and I keep getting illegal
instruction: 4 (here is the output)
/Applications/freesurfer/python/scripts/mri_sclimbi
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