Re: [Freesurfer] etiv value differs if using recon all vs freesurfer dev

2022-07-28 Thread Miriam Taza 
External Email - Use Caution

new recon all: freesurfer-darwin-macOS-dev-20220328-fc008d0
old recon all: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N. Greve 

Sent: Thursday, July 28, 2022 2:05 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] etiv value differs if using recon all vs freesurfer 
dev

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<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Douglas N. Greve 
<mailto:dgr...@mgh.harvard.edu>
Sent: Thursday, July 28, 2022 1:27 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> 
<mailto: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>
 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Miriam Taza 
<mailto:miriam.t...@mail.mcgill.ca>
Sent: Monday, July 25, 2022 2:45 PM
To: Freesurfer support list 
<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>
 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Douglas N. Greve 
<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> 
<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 --

Re: [Freesurfer] etiv value differs if using recon all vs freesurfer dev

2022-07-28 Thread Douglas N. Greve 
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 
 on behalf of Douglas N. Greve 


*Sent:* Thursday, July 28, 2022 1:27 PM
*To:* 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> 
 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Miriam 
Taza  <mailto:miriam.t...@mail.mcgill.ca>

*Sent:* Monday, July 25, 2022 2:45 PM
*To:* Freesurfer support list  
<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> 
 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas 
N. Greve  <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> 
 <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

Re: [Freesurfer] etiv value differs if using recon all vs freesurfer dev

2022-07-28 Thread Miriam Taza 
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 
 on behalf of Douglas N. Greve 

Sent: Thursday, July 28, 2022 1:27 PM
To: 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>
 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Miriam Taza 
<mailto:miriam.t...@mail.mcgill.ca>
Sent: Monday, July 25, 2022 2:45 PM
To: Freesurfer support list 
<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>
 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Douglas N. Greve 
<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> 
<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?

[cid:part1.ZsO56paS.r3IDc4tc@mgh.harvard.edu]
Thank you!



___
Freesurfer mailing list

Re: [Freesurfer] etiv value differs if using recon all vs freesurfer dev

2022-07-28 Thread Douglas N. Greve 

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 
 on behalf of Miriam Taza 


*Sent:* Monday, July 25, 2022 2:45 PM
*To:* Freesurfer support list 
*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 
 on behalf of Douglas N. Greve 


*Sent:* Sunday, July 24, 2022 10:38 PM
*To:* 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!

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu  <mailto:Freesurfer@nmr.mgh.harvard.edu>
*MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be* 
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer  <https://secure-web.cisco.com/1rESAy3sHUtcd743gY9Au36Y3WAA9bSghcjlCIeVtOsL1jsFgpO__SF3g9k1iqtvfo1nEKsadwuMAzwbKaS7V4ILPiu0tQQEZf8K6Xaye-v01D93NX0BWYoFEFLXpUWADHUwh_qgvYDJUQE7vRr4iLWqsJ8OZ0751aJq9dcf89OwPDd-KzgASIxR9xgrAr8PLsRLwdFoYEYzlBnmKUKEbsR0mVWwOADFykTtJvaKyfEb9ec-0TanwEoM-r4GNb2PIIQlk3iaS_sZbVVRW0DURMkcLrtTx9HpVX42ZVymQuGAQrjd85wnQq7uSS_JqXKfy4Qz6YXTJljG5TijuAWkD-w/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>



___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.e

Re: [Freesurfer] etiv value differs if using recon all vs freesurfer dev

2022-07-25 Thread Miriam Taza 
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 
 on behalf of Miriam Taza 

Sent: Monday, July 25, 2022 2:45 PM
To: Freesurfer support list 
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 
 on behalf of Douglas N. Greve 

Sent: Sunday, July 24, 2022 10:38 PM
To: 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?

[cid:part1.sA3Rabfi.kQu6g3TD@mgh.harvard.edu]
Thank you!



___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
https://secure-web.cisco.com/1tK7cz4Bgz05agttRXwn7g7tBXMKhxio5vaGu4KBxGeCKO3xbBawvTHbGkr_CZrD7pltdR8pVU1kCTpKHXSI7P1_20G80Dbl72eOv_QFGFoaMO3Mqd_oC3RX_icWYu2Q84u2NAkdyOHK8DtSgEhByEX3NbwUpzb1ehcAG_VcE4OTqji67uoVNgy3hoW7gmNt-cDAyHOwr1dcpE66C79HMBpYVEy89pPqaJlZ5J79DPkNguigxfEViUxBZalPQi6NWuSn1XaeSPTpTyeyDhTFmbi4sJZ8TbnZExRjR9gEq-vtuichIGYtdlX6I4srq8cje/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer<https://secure-web.cisco.com/1rESAy3sHUtcd743gY9Au36Y3WAA9bSghcjlCIeVtOsL1jsFgpO__SF3g9k1iqtvfo1nEKsadwuMAzwbKaS7V4ILPiu0tQQEZf8K6Xaye-v01D93NX0BWYoFEFLXpUWADHUwh_qgvYDJUQE7vRr4iLWqsJ8OZ0751aJq9dcf89OwPDd-KzgASIxR9xgrAr8PLsRLwdFoYEYzlBnmKUKEbsR0mVWwOADFykTtJvaKyfEb9ec-0TanwEoM-r4GNb2PIIQlk3iaS_sZbVVRW0DURMkcLrtTx9HpVX42ZVymQuGAQrjd85wnQq7uSS_JqXKfy4Qz6YXTJljG5TijuAWkD-w/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>

__

Re: [Freesurfer] etiv value differs if using recon all vs freesurfer dev

2022-07-25 Thread Douglas N. Greve 


On 7/25/2022 2:45 PM, Miriam Taza wrote:


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
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 
 on behalf of Douglas N. Greve 


*Sent:* Sunday, July 24, 2022 10:38 PM
*To:* 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!

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu  <mailto:Freesurfer@nmr.mgh.harvard.edu>
*MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be* 
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer  <https://secure-web.cisco.com/1rESAy3sHUtcd743gY9Au36Y3WAA9bSghcjlCIeVtOsL1jsFgpO__SF3g9k1iqtvfo1nEKsadwuMAzwbKaS7V4ILPiu0tQQEZf8K6Xaye-v01D93NX0BWYoFEFLXpUWADHUwh_qgvYDJUQE7vRr4iLWqsJ8OZ0751aJq9dcf89OwPDd-KzgASIxR9xgrAr8PLsRLwdFoYEYzlBnmKUKEbsR0mVWwOADFykTtJvaKyfEb9ec-0TanwEoM-r4GNb2PIIQlk3iaS_sZbVVRW0DURMkcLrtTx9HpVX42ZVymQuGAQrjd85wnQq7uSS_JqXKfy4Qz6YXTJljG5TijuAWkD-w/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>



___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
<https://www.massgeneralbrigham.org/complianceline> .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.

Re: [Freesurfer] etiv value differs if using recon all vs freesurfer dev

2022-07-25 Thread Miriam Taza 
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 
 on behalf of Douglas N. Greve 

Sent: Sunday, July 24, 2022 10:38 PM
To: 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?

[cid:part1.sA3Rabfi.kQu6g3TD@mgh.harvard.edu]
Thank you!



___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
https://secure-web.cisco.com/1rESAy3sHUtcd743gY9Au36Y3WAA9bSghcjlCIeVtOsL1jsFgpO__SF3g9k1iqtvfo1nEKsadwuMAzwbKaS7V4ILPiu0tQQEZf8K6Xaye-v01D93NX0BWYoFEFLXpUWADHUwh_qgvYDJUQE7vRr4iLWqsJ8OZ0751aJq9dcf89OwPDd-KzgASIxR9xgrAr8PLsRLwdFoYEYzlBnmKUKEbsR0mVWwOADFykTtJvaKyfEb9ec-0TanwEoM-r4GNb2PIIQlk3iaS_sZbVVRW0DURMkcLrtTx9HpVX42ZVymQuGAQrjd85wnQq7uSS_JqXKfy4Qz6YXTJljG5TijuAWkD-w/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
<https://www.massgeneralbrigham.org/complianceline> .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.

Re: [Freesurfer] etiv value differs if using recon all vs freesurfer dev

2022-07-24 Thread Douglas N. Greve 
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!

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.

[Freesurfer] etiv value differs if using recon all vs freesurfer dev

2022-07-24 Thread Miriam Taza 
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?

[cid:37ebf2b4-95b9-4b28-8fe6-86715ee89d72]
Thank you!
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.