The "cvs_version" is just for that particular binary. look in
$FREESURFER_HOME/build-stamp.txt. There should also be a build stamp
file in $SUBJECTS_DIR/subject/scripts (should be in the recon-all.log too)
On 7/28/2022 1:41 PM, Miriam Taza wrote:
External Email - Use Caution
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 also have
this: freesurfer-darwin-macOS-dev-20220328-fc008d0
How do i check the old recon all? It was done in the past.is there a log?
------------------------------------------------------------------------
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve
<dgr...@mgh.harvard.edu>
*Sent:* Thursday, July 28, 2022 1:27 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
What version of FS are you using for recon-all?
On 7/25/2022 9:45 PM, Miriam Taza wrote:
External Email - Use Caution
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
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu>
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Miriam
Taza <miriam.t...@mail.mcgill.ca> <mailto:miriam.t...@mail.mcgill.ca>
*Sent:* Monday, July 25, 2022 2:45 PM
*To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
<mailto:freesurfer@nmr.mgh.harvard.edu>
*Subject:* Re: [Freesurfer] etiv value differs if using recon all vs
freesurfer dev
External Email - Use Caution
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
<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:* Sunday, July 24, 2022 10:38 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] 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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