Re: [Freesurfer] mri_segstats error:

[Huang, Yujing]

Hi Brooklyn,

Can you check your recon-all command? Can you attach the recon-all.log?

>From your message, it reads "recon-al1 -s cor 15".  It should be recon-all. 
>There is also a space in your subject name.

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Brooklyn Wright
Sent: Wednesday, January 4, 2023 9:17 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] mri_segstats error:


External Email - Use Caution
Hello Freesurfer Developers,

I am currently trying to perform reconstructions on 1mm^3 T1 data and am 
finding this error towards the end of the processing;


\n mri brainvol _stats cor. 15 \n

Segmentation fault

Darwin UW-C02L2083DNMP 18.7.0 Darwin Kernel Version 18.7.0: Tue Jun 22 19:37:08 
PDT 2021; root:xnu-4903.278.79-1/RELEASE_X86_ 64 x86_64

recon-al1 -s cor 15 exited with ERRORS at Tue Dec 20 11:16:05 AEDT 2022

Do you know why this is happening and how to fix this?

Kindest,
Brooklyn.
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[Freesurfer] mri_segstats error:

[Brooklyn Wright]

External Email - Use Caution

Hello Freesurfer Developers,

I am currently trying to perform reconstructions on 1mm^3 T1 data and am 
finding this error towards the end of the processing;


\n mri brainvol _stats cor. 15 \n

Segmentation fault

Darwin UW-C02L2083DNMP 18.7.0 Darwin Kernel Version 18.7.0: Tue Jun 22 19:37:08 
PDT 2021; root:xnu-4903.278.79-1/RELEASE_X86_ 64 x86_64

recon-al1 -s cor 15 exited with ERRORS at Tue Dec 20 11:16:05 AEDT 2022

Do you know why this is happening and how to fix this?

Kindest,
Brooklyn.
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 .
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Re: [Freesurfer] mri_segstats error

[Douglas N Greve]

The ICV will not change because that depends on the talairach transform. 
mri_segstats just reads in the transform that is there and computes the 
ICV (note that this is an *estimated* ICV, it is not derived by counting 
voxels). There have been several bugs with mri_segstats that are 
difficult to explain. Most of them have to do with making small 
adjustments to the various brain volume measurements (not ICV), and 
there was a fix to the partial volume correction too. The new version 
will change all of the measurements (except ICV).

doug

On 08/23/2012 08:31 PM, Natalie Han wrote:
 Hi, Doug and all, I wonder if the new version of mri_segstats on the ftp site
 will change both the ICV and the SupraTentorial volume? Nick seems to
 mention ICV will be different, the ReleaseNotes says the
 SupraTentorial Volume will be changed to smaller. Can you explain more
 on the difference of the new version with the original version in
 FS.5.1.0? Is everything on the morphometry stats website still the
 same? http://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats. I'm
 interested in several measurements, including the ICV, and the
 SupraTentorial Volume and all the structures volume, just wondering if
 the new version will change all the measurements.

 Thanks.
 -Natalie

 On Wed, Aug 22, 2012 at 8:57 AM, Douglas N Greve
 gr...@nmr.mgh.harvard.edu  wrote:
 yes, this is a fix that will be in the next release. The new results are
 more accurate.
 doug

 On 08/22/2012 11:54 AM, Blazey, Tyler wrote:
 Hi Doug,

 Thanks for the quickly reply. The new version of mri_segstats works fine. I 
 noticed after running it though that all the volumes are slightly different 
 than those reported by previous version. I think it might have something to 
 do with the partial volume correction, as the results are the same when I 
 do not use the --pv flag. Is this expected behavior? And if so, is the new 
 version more accurate?

 Thanks again,

 -Tyler



 

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 action in reliance on the contents of this information is strictly 
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 gr...@nmr.mgh.harvard.edu
 Phone Number: 617-724-2358
 Fax: 617-726-7422

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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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Re: [Freesurfer] mri_segstats error

[Natalie Han]

Hi, Doug and all, I wonder if the new version of mri_segstats on the ftp site
will change both the ICV and the SupraTentorial volume? Nick seems to
mention ICV will be different, the ReleaseNotes says the
SupraTentorial Volume will be changed to smaller. Can you explain more
on the difference of the new version with the original version in
FS.5.1.0? Is everything on the morphometry stats website still the
same? http://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats. I'm
interested in several measurements, including the ICV, and the
SupraTentorial Volume and all the structures volume, just wondering if
the new version will change all the measurements.

Thanks.
-Natalie

On Wed, Aug 22, 2012 at 8:57 AM, Douglas N Greve
gr...@nmr.mgh.harvard.edu wrote:
 yes, this is a fix that will be in the next release. The new results are
 more accurate.
 doug

 On 08/22/2012 11:54 AM, Blazey, Tyler wrote:
 Hi Doug,

 Thanks for the quickly reply. The new version of mri_segstats works fine. I 
 noticed after running it though that all the volumes are slightly different 
 than those reported by previous version. I think it might have something to 
 do with the partial volume correction, as the results are the same when I do 
 not use the --pv flag. Is this expected behavior? And if so, is the new 
 version more accurate?

 Thanks again,

 -Tyler



 

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 Information (PHI). If you are not the intended recipient, be advised that 
 any unauthorized use, disclosure, copying or the taking of any action in 
 reliance on the contents of this information is strictly prohibited. If you 
 have received this email in error, please immediately notify the sender via 
 telephone or return mail.

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 MGH-NMR Center
 gr...@nmr.mgh.harvard.edu
 Phone Number: 617-724-2358
 Fax: 617-726-7422

 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Re: [Freesurfer] mri_segstats error

[Blazey, Tyler]

Hi Doug,

Thanks for the quickly reply. The new version of mri_segstats works fine. I 
noticed after running it though that all the volumes are slightly different 
than those reported by previous version. I think it might have something to do 
with the partial volume correction, as the results are the same when I do not 
use the --pv flag. Is this expected behavior? And if so, is the new version 
more accurate?

Thanks again,

-Tyler





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telephone or return mail.

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Re: [Freesurfer] mri_segstats error

[Douglas N Greve]

yes, this is a fix that will be in the next release. The new results are 
more accurate.
doug

On 08/22/2012 11:54 AM, Blazey, Tyler wrote:
 Hi Doug,

 Thanks for the quickly reply. The new version of mri_segstats works fine. I 
 noticed after running it though that all the volumes are slightly different 
 than those reported by previous version. I think it might have something to 
 do with the partial volume correction, as the results are the same when I do 
 not use the --pv flag. Is this expected behavior? And if so, is the new 
 version more accurate?

 Thanks again,

 -Tyler



 

 The material in this message is private and may contain Protected Healthcare 
 Information (PHI). If you are not the intended recipient, be advised that any 
 unauthorized use, disclosure, copying or the taking of any action in reliance 
 on the contents of this information is strictly prohibited. If you have 
 received this email in error, please immediately notify the sender via 
 telephone or return mail.

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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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[Freesurfer] mri_segstats error

[Blazey, Tyler]

Hi,

I recently installed the updated mri_segstats 
(ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_segstats.linux).
 This seems to work fine for recalculating the supratentorial volume. However, 
it is causing my new recons to fail (see example error below). Any suggestions?

Thanks,

-Tyler

$Id: mri_segstats.c,v 1.86 2012/07/16 14:39:07 greve Exp $
cwd
cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.24644/ones.mgz --i 
./tmp.mri_nu_correct.mni.24644/nu2.mnc --sum 
./tmp.mri_nu_correct.mni.24644/sum.junk --avgwf 
./tmp.mri_nu_correct.mni.24644/output.mean.dat
sysname  Linux
hostname login001
machine  x86_64
user tblazey
UseRobust  0
Loading ./tmp.mri_nu_correct.mni.24644/ones.mgz
Loading ./tmp.mri_nu_correct.mni.24644/nu2.mnc
Voxel Volume is 1 mm^3
Generating list of segmentation ids
Found   1 segmentations
Computing statistics for each segmentation
  0 1  0  0

Reporting on   0 segmentations
Computing spatial average of each frame

Writing to ./tmp.mri_nu_correct.mni.24644/output.mean.dat
(standard_in) 1: parse error





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Re: [Freesurfer] mri_segstats error

[Douglas N Greve]

Sorry, there was a bug in that version. I've put an updated version on 
that ftp site
doug

On 08/21/2012 03:49 PM, Blazey, Tyler wrote:
 Hi,

 I recently installed the updated mri_segstats 
 (ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_segstats.linux).
  
 This seems to work fine for recalculating the supratentorial volume. 
 However, it is causing my new recons to fail (see example error 
 below). Any suggestions?

 Thanks,

 -Tyler

 $Id: mri_segstats.c,v 1.86 2012/07/16 14:39:07 greve Exp $
 cwd
 cmdline mri_segstats --id 1 --seg 
 ./tmp.mri_nu_correct.mni.24644/ones.mgz --i 
 ./tmp.mri_nu_correct.mni.24644/nu2.mnc --sum 
 ./tmp.mri_nu_correct.mni.24644/sum.junk --avgwf 
 ./tmp.mri_nu_correct.mni.24644/output.mean.dat
 sysname  Linux
 hostname login001
 machine  x86_64
 user tblazey
 UseRobust  0
 Loading ./tmp.mri_nu_correct.mni.24644/ones.mgz
 Loading ./tmp.mri_nu_correct.mni.24644/nu2.mnc
 Voxel Volume is 1 mm^3
 Generating list of segmentation ids
 Found   1 segmentations
 Computing statistics for each segmentation
   0 1  0  0

 Reporting on   0 segmentations
 Computing spatial average of each frame

 Writing to ./tmp.mri_nu_correct.mni.24644/output.mean.dat
 (standard_in) 1: parse error



 

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 be advised that any unauthorized use, disclosure, copying or the 
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 is strictly prohibited. If you have received this email in error, 
 please immediately notify the sender via telephone or return mail.


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-- 
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gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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[Freesurfer] mri_segstats error

[Fernanda Palhano]

Hello,

I'm trying to use mri_segstats to obtain some subcortical volume stats. When
running the command line both in the tutorial data or in my own data, I have
the follow error: ERROR: could not open stats/aseg.stats for writing

[Fernanda-Palhanos-Mac-Pro:buckner_data/tutorial_subjs/group_analysis_tutorial]
fernandapalhano% mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv
mri/norm.mgz --ctab-default --excludeid 0 --brain-vol-from-seg --brainmask
mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm
--in-intensity-units MR --etiv --subject 004
Using defalt ctab /Applications/freesurfer/FreeSurferColorLUT.txt

$Id: mri_segstats.c,v 1.69.2.1 2010/07/26 16:19:29 greve Exp $
cwd
cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv
mri/norm.mgz --ctab-default --excludeid 0 --brain-vol-from-seg --brainmask
mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm
--in-intensity-units MR --etiv --subject 004
sysname  Darwin
hostname Fernanda-Palhanos-Mac-Pro.local
machine  i386
user fernandapalhano
atlas_icv (eTIV) = 1792580 mm^3(det: 1.086761 )
ERROR: could not open stats/aseg.stats for writing

Any ideas?

Thanks,
Fernanda
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Re: [Freesurfer] mri_segstats error

[Douglas N Greve]

does the stats directory exist?
doug

Fernanda Palhano wrote:
 Hello,

 I'm trying to use mri_segstats to obtain some subcortical volume 
 stats. When running the command line both in the tutorial data or in 
 my own data, I have the follow error: ERROR: could not open 
 stats/aseg.stats for writing

 [Fernanda-Palhanos-Mac-Pro:buckner_data/tutorial_subjs/group_analysis_tutorial]
  
 fernandapalhano% mri_segstats --seg mri/aseg.mgz --sum 
 stats/aseg.stats --pv mri/norm.mgz --ctab-default --excludeid 0 
 --brain-vol-from-seg --brainmask mri/brainmask.mgz --in mri/norm.mgz 
 --in-intensity-name norm --in-intensity-units MR --etiv --subject 004
 Using defalt ctab /Applications/freesurfer/FreeSurferColorLUT.txt

 $Id: mri_segstats.c,v 1.69.2.1 2010/07/26 16:19:29 greve Exp $
 cwd
 cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv 
 mri/norm.mgz --ctab-default --excludeid 0 --brain-vol-from-seg 
 --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name 
 norm --in-intensity-units MR --etiv --subject 004
 sysname  Darwin
 hostname Fernanda-Palhanos-Mac-Pro.local
 machine  i386
 user fernandapalhano
 atlas_icv (eTIV) = 1792580 mm^3(det: 1.086761 )
 ERROR: could not open stats/aseg.stats for writing

 Any ideas?

 Thanks,
 Fernanda
 

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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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Re: [Freesurfer] mri_segstats error

[Douglas N Greve]

And do you have write permissions? Can you
touch stats/aseg.stats

doug

Fernanda Palhano wrote:
 Yes.

 [Fernanda-Palhanos-Mac-Pro:group_analysis_tutorial/004/stats] 
 fernandapalhano% ls
 aseg.statslh.aparc.a2009s.statslh.supramarg.stats
 rh.aparc.a2009s.statswmparc.stats
 lh.aparc.a2005s.statslh.aparc.stats
 rh.aparc.a2005s.statsrh.aparc.stats

 Fernanda

 On Mon, May 16, 2011 at 4:07 PM, Douglas N Greve 
 gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote:

 does the stats directory exist?
 doug

 Fernanda Palhano wrote:

 Hello,

 I'm trying to use mri_segstats to obtain some subcortical
 volume stats. When running the command line both in the
 tutorial data or in my own data, I have the follow error:
 ERROR: could not open stats/aseg.stats for writing

 
 [Fernanda-Palhanos-Mac-Pro:buckner_data/tutorial_subjs/group_analysis_tutorial]
 fernandapalhano% mri_segstats --seg mri/aseg.mgz --sum
 stats/aseg.stats --pv mri/norm.mgz --ctab-default --excludeid
 0 --brain-vol-from-seg --brainmask mri/brainmask.mgz --in
 mri/norm.mgz --in-intensity-name norm --in-intensity-units MR
 --etiv --subject 004
 Using defalt ctab /Applications/freesurfer/FreeSurferColorLUT.txt

 $Id: mri_segstats.c,v 1.69.2.1 2010/07/26 16:19:29 greve Exp $
 cwd
 cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats
 --pv mri/norm.mgz --ctab-default --excludeid 0
 --brain-vol-from-seg --brainmask mri/brainmask.mgz --in
 mri/norm.mgz --in-intensity-name norm --in-intensity-units MR
 --etiv --subject 004
 sysname  Darwin
 hostname Fernanda-Palhanos-Mac-Pro.local
 machine  i386
 user fernandapalhano
 atlas_icv (eTIV) = 1792580 mm^3(det: 1.086761 )
 ERROR: could not open stats/aseg.stats for writing

 Any ideas?

 Thanks,
 Fernanda
 
 

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 -- 
 Douglas N. Greve, Ph.D.
 MGH-NMR Center
 gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu
 Phone Number: 617-724-2358 Fax: 617-726-7422

 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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Re: [Freesurfer] mri_segstats error

[Douglas N Greve]

yes, that is fine.
doug

Fernanda Palhano wrote:
 Doug,

 I have another question about doing a volumetric group analysis. I 
 used the command:
 asegstats2table --subjects V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11 V12 V13 
 V14 V15 V16 V17 V18 V19 V20 V21 V22 V23 V24 V25 V26 V27 V28 V29 V30 
 V31 V32 --tablefile asegstats_new.txt --common-segs
 To extract volume information for all my subjects. I'm interested in 
 use Left-Hippocampus and Right-Hippocampus to perform my group 
 analysis. Is it correct just import the columns data ( 
 Left-Hippocampus and Right-Hippocampus) in some statistical software?

 Thanks a lot,
 Fernanda

 On Mon, May 16, 2011 at 4:25 PM, Fernanda Palhano 
 nandapalh...@gmail.com mailto:nandapalh...@gmail.com wrote:

 Doug,

 Actually, the file aseg.stats already exists. I think I only have
 to use asegstats2table
 http://surfer.nmr.mgh.harvard.edu/fswiki/asegstats2table to
 combine the stats from all my subjects.


 Fernanda


 On Mon, May 16, 2011 at 4:15 PM, Fernanda Palhano
 nandapalh...@gmail.com mailto:nandapalh...@gmail.com wrote:

 Yes.

 [Fernanda-Palhanos-Mac-Pro:group_analysis_tutorial/004/stats]
 fernandapalhano% ls
 aseg.statslh.aparc.a2009s.stats   
 lh.supramarg.statsrh.aparc.a2009s.statswmparc.stats
 lh.aparc.a2005s.statslh.aparc.stats   
 rh.aparc.a2005s.statsrh.aparc.stats

 Fernanda


 On Mon, May 16, 2011 at 4:07 PM, Douglas N Greve
 gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu
 wrote:

 does the stats directory exist?
 doug

 Fernanda Palhano wrote:

 Hello,

 I'm trying to use mri_segstats to obtain some
 subcortical volume stats. When running the command
 line both in the tutorial data or in my own data, I
 have the follow error: ERROR: could not open
 stats/aseg.stats for writing

 
 [Fernanda-Palhanos-Mac-Pro:buckner_data/tutorial_subjs/group_analysis_tutorial]
 fernandapalhano% mri_segstats --seg mri/aseg.mgz --sum
 stats/aseg.stats --pv mri/norm.mgz --ctab-default
 --excludeid 0 --brain-vol-from-seg --brainmask
 mri/brainmask.mgz --in mri/norm.mgz
 --in-intensity-name norm --in-intensity-units MR
 --etiv --subject 004
 Using defalt ctab
 /Applications/freesurfer/FreeSurferColorLUT.txt

 $Id: mri_segstats.c,v 1.69.2.1 2010/07/26 16:19:29
 greve Exp $
 cwd
 cmdline mri_segstats --seg mri/aseg.mgz --sum
 stats/aseg.stats --pv mri/norm.mgz --ctab-default
 --excludeid 0 --brain-vol-from-seg --brainmask
 mri/brainmask.mgz --in mri/norm.mgz
 --in-intensity-name norm --in-intensity-units MR
 --etiv --subject 004
 sysname  Darwin
 hostname Fernanda-Palhanos-Mac-Pro.local
 machine  i386
 user fernandapalhano
 atlas_icv (eTIV) = 1792580 mm^3(det: 1.086761 )
 ERROR: could not open stats/aseg.stats for writing

 Any ideas?

 Thanks,
 Fernanda
 
 

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 -- 
 Douglas N. Greve, Ph.D.
 MGH-NMR Center
 gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu
 Phone Number: 617-724-2358 Fax: 617-726-7422

 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 FileDrop:
 www.nmr.mgh.harvard.edu/facility/filedrop/index.html
 http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html



 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 Partners
 Compliance HelpLine at
 http://www.partners.org/complianceline . If the e-mail was
 sent to you in error
 but does not contain patient information, please contact
 the sender and properly
 dispose of the e-mail.





-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone