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 all and the sclimbic output (although it is closer to
sclimbic).
Here is the log for both recon all.
original recon all, etiv = *1169944.199744*
# cvs_version $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11
greve Exp $
# cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats
--pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz
--brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent
--subcortgray --in mri/norm.mgz --in-intensity-name norm
--in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol
--totalgray --euler --ctab /opt/freesurfer/ASegStatsLUT.txt
--subject sub-1221084
# SegVolFileTimeStamp 2018/02/28 00:18:52
new etiv = *702243.513916*
# cvs_version dev
# cmdline mri_segstats --seed 1234 --seg mri/aseg.mgz --sum
stats/aseg.stats --pv mri/norm.mgz --empty --brainmask
mri/brainmask.mgz --brain-vol-from-seg --excludeid 0
--excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz
--in-intensity-name norm --in-intensity-units MR --etiv
--surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab
/Applications/freesurfer/ASegStatsLUT.txt --subject sub-1221084
# SegVolFileTimeStamp 2022/07/25 21:04:31
sclimbic etiv= *686180.089200
*
*
*
>From a quick glance, the other values dont seem to differ by much
between recons so I'm not sure 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
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Miriam Taza
<miriam.t...@mail.mcgill.ca>
*Sent:* Monday, July 25, 2022 2:45 PM
*To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
*Subject:* Re: [Freesurfer] etiv value differs if using recon all vs
freesurfer dev
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I am getting eerror: mri_segstats: could not open atlas transform file
/export01/local/freesurfer/subjects/sub-1221084/mri/transforms/talairach.xfm
The results do agree when Re running sclimbic.
it seems that when etiv differs a bit from the median, sclimbic module
calculates etiv to an extreme.
Is this expected to happen? I am concerned if my volumes are incorrect.
------------------------------------------------------------------------
*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, July 24, 2022 10:38 PM
*To:* freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
*Subject:* Re: [Freesurfer] etiv value differs if using recon all vs
freesurfer dev
I cannot replicate this on my data. The differences are rather extreme
(factors of 3). Can you get us access to the one with the largest
difference? YOu can also try regenerating the aseg.stats file, eg,
cd subject/
mri_segstats --seed 1234 --seg mri/aseg.mgz --sum
stats/redo.aseg.stats --pv mri/norm.mgz --empty --brainmask
mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm
--supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm
--in-intensity-units MR --etiv --surf-wm-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:
External Email - Use Caution
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 tighter (see attached). Why is
there this discrepancy and what do you recommend?
Thank you!
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