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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.

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From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgreve@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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