Hello,
The files didnt work!
Here is the error after trying 2 participants, one with each mri_segstats you attached.
same error for both.
Could you please let me know what to do next?
n#-----------------------------------------
#@# Curvature Stats rh Tue May 24 08:13:18 JST 2016
/Users/dave/Documents/tot/Studies/ASD_Struct/Kj/Surf_test/PSY1012fs/surf
\n mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm PSY1012fs rh curv sulc \n
Toggling save flag on curvature files [ ok ]
Outputting results using filestem [ ../stats/rh.curv.stats ]
Toggling save flag on curvature files [ ok ]
Setting surface [ PSY1012fs/rh.smoothwm ]
Reading surface... [ ok ]
Setting texture [ curv ]
Reading texture... [ ok ]
Setting texture [ sulc ]
Reading texture...Gb_filter = 0
[ ok ]
Calculating Discrete Principal Curvatures...
Determining geometric order for vertex faces... [####################] [ ok ]
Determining KH curvatures... [####################] [ ok ]
Determining k1k2 curvatures... [####################] [ ok ]
deltaViolations [ 260 ]
Gb_filter = 0
WARN: S lookup min: -0.175830
WARN: S explicit min: 0.000000 vertex = 422
#--------------------------------------------
#@# ASeg Stats Tue May 24 08:13:23 JST 2016
\nINFO: mri_segstats will not calculate Supratentorial
due to missing ribbon.mgz file
/Users/dave/Documents/tot/Studies/ASD_Struct/kj/Surf_test/PSY1012fs
\n 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 --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 PSY1012fs \n
$Id: mri_segstats.c,v 1.110.2.3 2015/07/02 20:12:19 zkaufman Exp $
cwd
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 --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 PSY1012fs
sysname Darwin
hostname daves-Mac-Pro.local
machine x86_64
user dave
UseRobust 0
atlas_icv (eTIV) = 1512862 mm^3 (det: 1.287696 )
Computing euler number
orig.nofix lheno = -122, rheno = -128
orig.nofix lhholes = 62, rhholes = 65
Loading mri/aseg.mgz
Warning: cannot find /Users/dave/Documents/tot/Studies/ASD_Struct/kj/Surf_test/PSY1012fs/mri/ribbon.mgz, not computing whole brain stats
Loading mri/norm.mgz
Loading mri/norm.mgz
Voxel Volume is 1 mm^3
Generating list of segmentation ids
Found 50 segmentations
Computing statistics for each segmentation
Reporting on 45 segmentations
Using PrintSegStat
mri_segstats done
#------------------------------------------
Started at Mon May 23 11:43:42 JST 2016
Ended at Tue May 24 08:16:38 JST 2016
#@#%# recon-all-run-time-hours 20.549
recon-all -s PSY1012fs finished without error at Tue May 24 08:16:38 JST 2016
done
[daves-Mac-Pro:ASD_Struct/kj/Surf_test] dave%
From: davemania@hotmail.com
To: freesurfer@nmr.mgh.harvard.edu
Date: Fri, 20 May 2016 01:07:28 +0000
Subject: Re: [Freesurfer] The results of your email commands
Thanks a lot.
Does the snowleaopard version work on El Capitan?
So by replacing the version already found in bin/mrisegstats, with the leopard one after Chomd +x, it should work?
I thought i would get a link for something like mri_segstats.ElCapitan?
Yas
> To: freesurfer@nmr.mgh.harvard.edu
> From: greve@nmr.mgh.harvard.edu
> Date: Thu, 19 May 2016 11:07:40 -0400
> Subject: Re: [Freesurfer] The results of your email commands
>
> I've refreshed those links
>
> On 05/18/2016 10:44 PM, Dave Yas wrote:
> > Dear Doug,
> >
> > I'm getting mri_segstats error [mghread(...ribbon.mgz) at the end of
> > -autorecon2.
> > I saw your answer for others about this Q before and i know how to
> > solve this *IF* i was able to access to the links you posted.
> >
> > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_segstats.centos6
> > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_segstats.snowleopard
> >
> > I thought that these should give me some kind of a pop up to prompt me
> > to enter as a guest and get the file to put it in bin/mrisegstats
> > But its not doesin anything.
> > Also im running OSX El capitan.
> > Is there any link that i can visit to download the missing mrisegstats
> > file?
> >
> > Thanks,
> >
> > Yas
> >
> >
> >
> >
> > _______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> greve@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> _______________________________________________
> 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 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.
>
> From: greve@nmr.mgh.harvard.edu
> Date: Thu, 19 May 2016 11:07:40 -0400
> Subject: Re: [Freesurfer] The results of your email commands
>
> I've refreshed those links
>
> On 05/18/2016 10:44 PM, Dave Yas wrote:
> > Dear Doug,
> >
> > I'm getting mri_segstats error [mghread(...ribbon.mgz) at the end of
> > -autorecon2.
> > I saw your answer for others about this Q before and i know how to
> > solve this *IF* i was able to access to the links you posted.
> >
> > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_segstats.centos6
> > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_segstats.snowleopard
> >
> > I thought that these should give me some kind of a pop up to prompt me
> > to enter as a guest and get the file to put it in bin/mrisegstats
> > But its not doesin anything.
> > Also im running OSX El capitan.
> > Is there any link that i can visit to download the missing mrisegstats
> > file?
> >
> > Thanks,
> >
> > Yas
> >
> >
> >
> >
> > _______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> greve@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> _______________________________________________
> 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 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.
>
_______________________________________________ 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 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.