On 7/25/2022 2:45 PM, Miriam Taza wrote:
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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
does
/export01/local/freesurfer/subjects/sub-1221084/mri/transforms/talairach.xfm
exist? If not, do you have your SUBJECTS_DIR set properly?
The results do agree when Re running sclimbic.
what agrees with what?
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.
I don't know what you mean. The eTIV in mri_sclimbic_seg should agree
nearly perfectly to that in aseg.stats
------------------------------------------------------------------------
*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:
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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 tighter (see attached). Why is
there this discrepancy and what do you recommend?
Thank you!
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