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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?
[cid:37ebf2b4-95b9-4b28-8fe6-86715ee89d72] Thank you!
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
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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-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:
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.edumailto:Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1rESAy3sHUtcd743gY9Au36Y3WAA9bSghcjlCIeVtOsL1js...
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-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:
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
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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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Miriam Taza miriam.taza@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-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:
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.edumailto: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/1tK7cz4Bgz05agttRXwn7g7tBXMKhxio5vaGu4KBxGeCKO3...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
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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Miriam Taza miriam.taza@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-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:
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
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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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Miriam Taza miriam.taza@mail.mcgill.camailto:miriam.taza@mail.mcgill.ca Sent: Monday, July 25, 2022 2:45 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto: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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Sent: Sunday, July 24, 2022 10:38 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto: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!
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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:
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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 devif 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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@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:
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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-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Miriam Taza miriam.taza@mail.mcgill.ca mailto:miriam.taza@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
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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-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu mailto:dgreve@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:
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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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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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu Sent: Thursday, July 28, 2022 2:05 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
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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Sent: Thursday, July 28, 2022 1:27 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto: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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Miriam Taza miriam.taza@mail.mcgill.camailto:miriam.taza@mail.mcgill.ca Sent: Monday, July 25, 2022 2:45 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto: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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Sent: Sunday, July 24, 2022 10:38 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto: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.W30Xu4ic.XDOU099a@mgh.harvard.edu] Thank you!
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freesurfer@nmr.mgh.harvard.edu
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Douglas N. Greve -
Miriam Taza