Re: [Freesurfer] missing ribbon.mgz
External Email - Use Caution I just noticed that this problem is a now and resolved. I just have to replace the mri_segstats. Thank you for your time. On Fri, Jul 13, 2018 at 6:08 PM Aaron Tanenbaum wrote: > Yes, I first ran autorecon1 and 2 for the initial processing. I then made > only made brainmask edits followed by running it with autorecon2. The thing > is that according to this URL > >> https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable >> > > The ribbon.mgz is created in autorecon3, for this reason the file does not > exist. So why is it being called autorecon2? > > On Fri, Jul 13, 2018 at 5:27 PM Glasser, Matthew > wrote: > >> External Email - Use Caution >> >> Did you run the preceding steps of FreeSurfer? Does that file exist? >> >> Peace, >> >> Matt. >> >> From: on behalf of Aaron >> Tanenbaum >> Reply-To: Freesurfer support list >> Date: Friday, July 13, 2018 at 5:24 PM >> To: Freesurfer >> Subject: [Freesurfer] missing ribbon.mgz >> >> External Email - Use Caution >> >> I am a bit puzzled. I am running freesurfer 5.3 HCP on ubuntu 14.04. I >> am getting an error, see below >> I am using the command >> >> recon-all -s BOLD-52_v1 -mprage -autorecon2 >> This has happened before. What did I do wrong. >> >> >> >> #@# ASeg Stats Fri Jul 13 12:55:02 CDT 2018 >>> >>> INFO: mri_segstats will not calculate Supratentorial >>> due to missing ribbon.mgz file >>> /data/nil-bluearc/ances/Aaron/FreeSurfers/BOLD-52_v1 >>> >>> 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 >>> /data/ances/FreeSurfer/freesurfer_5_3_HCP//ASegStatsLUT.txt --subject >>> BOLD-52_v1 >>> >>> >>> $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve 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 >>> /data/ances/FreeSurfer/freesurfer_5_3_HCP//ASegStatsLUT.txt --subject >>> BOLD-52_v1 >>> sysname Linux >>> hostname brahms >>> machine x86_64 >>> user tanenbauma >>> UseRobust 0 >>> atlas_icv (eTIV) = 1714974 mm^3(det: 1.135939 ) >>> mghRead(/data/nil-bluearc/ances/Aaron/FreeSurfers/BOLD-52_v1/mri/ribbon.mgz, >>> -1): could not open file >>> Computing euler number >>> orig.nofix lheno = -70, rheno = -38 >>> orig.nofix lhholes = 36, rhholes = 20 >>> Loading mri/aseg.mgz >>> Getting Brain Volume Statistics >>> Linux brahms 3.19.0-80-generic #88~14.04.1-Ubuntu SMP Fri Jan 13 >>> 14:54:07 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux >>> >>> recon-all -s BOLD-52_v1 exited with ERRORS at Fri Jul 13 12:55:11 CDT >>> 2018 >>> >>> To report a problem, see >>> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>> >> >> >> >> >> >> -- >> >> The materials in this message are private and may contain Protected >> Healthcare Information or other information of a sensitive nature. 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. >> ___ >> 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.
Re: [Freesurfer] missing ribbon.mgz
External Email - Use Caution Yes, I first ran autorecon1 and 2 for the initial processing. I then made only made brainmask edits followed by running it with autorecon2. The thing is that according to this URL > https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable > The ribbon.mgz is created in autorecon3, for this reason the file does not exist. So why is it being called autorecon2? On Fri, Jul 13, 2018 at 5:27 PM Glasser, Matthew wrote: > External Email - Use Caution > > Did you run the preceding steps of FreeSurfer? Does that file exist? > > Peace, > > Matt. > > From: on behalf of Aaron > Tanenbaum > Reply-To: Freesurfer support list > Date: Friday, July 13, 2018 at 5:24 PM > To: Freesurfer > Subject: [Freesurfer] missing ribbon.mgz > > External Email - Use Caution > > I am a bit puzzled. I am running freesurfer 5.3 HCP on ubuntu 14.04. I am > getting an error, see below > I am using the command > > recon-all -s BOLD-52_v1 -mprage -autorecon2 > This has happened before. What did I do wrong. > > > > #@# ASeg Stats Fri Jul 13 12:55:02 CDT 2018 >> >> INFO: mri_segstats will not calculate Supratentorial >> due to missing ribbon.mgz file >> /data/nil-bluearc/ances/Aaron/FreeSurfers/BOLD-52_v1 >> >> 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 /data/ances/FreeSurfer/freesurfer_5_3_HCP//ASegStatsLUT.txt >> --subject BOLD-52_v1 >> >> >> $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve 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 >> /data/ances/FreeSurfer/freesurfer_5_3_HCP//ASegStatsLUT.txt --subject >> BOLD-52_v1 >> sysname Linux >> hostname brahms >> machine x86_64 >> user tanenbauma >> UseRobust 0 >> atlas_icv (eTIV) = 1714974 mm^3(det: 1.135939 ) >> mghRead(/data/nil-bluearc/ances/Aaron/FreeSurfers/BOLD-52_v1/mri/ribbon.mgz, >> -1): could not open file >> Computing euler number >> orig.nofix lheno = -70, rheno = -38 >> orig.nofix lhholes = 36, rhholes = 20 >> Loading mri/aseg.mgz >> Getting Brain Volume Statistics >> Linux brahms 3.19.0-80-generic #88~14.04.1-Ubuntu SMP Fri Jan 13 14:54:07 >> UTC 2017 x86_64 x86_64 x86_64 GNU/Linux >> >> recon-all -s BOLD-52_v1 exited with ERRORS at Fri Jul 13 12:55:11 CDT 2018 >> >> To report a problem, see >> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> > > > > > > -- > > The materials in this message are private and may contain Protected > Healthcare Information or other information of a sensitive nature. 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. > ___ > 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.
Re: [Freesurfer] missing ribbon.mgz
External Email - Use Caution Did you run the preceding steps of FreeSurfer? Does that file exist? Peace, Matt. From: mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Aaron Tanenbaum mailto:aaron.b.tanenb...@gmail.com>> Reply-To: Freesurfer support list mailto:Freesurfer@nmr.mgh.harvard.edu>> Date: Friday, July 13, 2018 at 5:24 PM To: Freesurfer mailto:Freesurfer@nmr.mgh.harvard.edu>> Subject: [Freesurfer] missing ribbon.mgz External Email - Use Caution I am a bit puzzled. I am running freesurfer 5.3 HCP on ubuntu 14.04. I am getting an error, see below I am using the command recon-all -s BOLD-52_v1 -mprage -autorecon2 This has happened before. What did I do wrong. #@# ASeg Stats Fri Jul 13 12:55:02 CDT 2018 INFO: mri_segstats will not calculate Supratentorial due to missing ribbon.mgz file /data/nil-bluearc/ances/Aaron/FreeSurfers/BOLD-52_v1 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 /data/ances/FreeSurfer/freesurfer_5_3_HCP//ASegStatsLUT.txt --subject BOLD-52_v1 $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve 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 /data/ances/FreeSurfer/freesurfer_5_3_HCP//ASegStatsLUT.txt --subject BOLD-52_v1 sysname Linux hostname brahms machine x86_64 user tanenbauma UseRobust 0 atlas_icv (eTIV) = 1714974 mm^3(det: 1.135939 ) mghRead(/data/nil-bluearc/ances/Aaron/FreeSurfers/BOLD-52_v1/mri/ribbon.mgz, -1): could not open file Computing euler number orig.nofix lheno = -70, rheno = -38 orig.nofix lhholes = 36, rhholes = 20 Loading mri/aseg.mgz Getting Brain Volume Statistics Linux brahms 3.19.0-80-generic #88~14.04.1-Ubuntu SMP Fri Jan 13 14:54:07 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux recon-all -s BOLD-52_v1 exited with ERRORS at Fri Jul 13 12:55:11 CDT 2018 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. 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. ___ 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] missing ribbon.mgz
External Email - Use Caution I am a bit puzzled. I am running freesurfer 5.3 HCP on ubuntu 14.04. I am getting an error, see below I am using the command recon-all -s BOLD-52_v1 -mprage -autorecon2 This has happened before. What did I do wrong. #@# ASeg Stats Fri Jul 13 12:55:02 CDT 2018 > > INFO: mri_segstats will not calculate Supratentorial > due to missing ribbon.mgz file > /data/nil-bluearc/ances/Aaron/FreeSurfers/BOLD-52_v1 > > 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 /data/ances/FreeSurfer/freesurfer_5_3_HCP//ASegStatsLUT.txt > --subject BOLD-52_v1 > > > $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve 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 > /data/ances/FreeSurfer/freesurfer_5_3_HCP//ASegStatsLUT.txt --subject > BOLD-52_v1 > sysname Linux > hostname brahms > machine x86_64 > user tanenbauma > UseRobust 0 > atlas_icv (eTIV) = 1714974 mm^3(det: 1.135939 ) > mghRead(/data/nil-bluearc/ances/Aaron/FreeSurfers/BOLD-52_v1/mri/ribbon.mgz, > -1): could not open file > Computing euler number > orig.nofix lheno = -70, rheno = -38 > orig.nofix lhholes = 36, rhholes = 20 > Loading mri/aseg.mgz > Getting Brain Volume Statistics > Linux brahms 3.19.0-80-generic #88~14.04.1-Ubuntu SMP Fri Jan 13 14:54:07 > UTC 2017 x86_64 x86_64 x86_64 GNU/Linux > > recon-all -s BOLD-52_v1 exited with ERRORS at Fri Jul 13 12:55:11 CDT 2018 > > To report a problem, see > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > ___ 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.
Re: [Freesurfer] Missing ribbon.mgz file
Dear Douglas, Thank you very much! Sincerely, Ye On Tue, Jul 2, 2013 at 10:36 AM, Douglas N Greve wrote: > > Hi Ye, one of the programs expects that recon-all will be run all the > way through instead of in parts. You will need to download a new version > of mri_segstats from > > > 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 > > Copy the file appropriate for your architecture to > $FREESURFER_HOME/bin/mri_segstats > > doug > > > > On 07/02/2013 11:31 AM, ye tian wrote: > > Dear freesurfers, > > > > Recon-all -s subject -autorecon2 returns the following error messages > > > > *mri_segstats will not calculate Supratentorial due to missing > > ribbon.mgz file* > > > > mghRead(Path_to_subject/mri/*ribbon.mgz, -1)*: could not open file. > > > > Prior to autorecon2, I did recon-all -s subject -autorecon1, which > > completed without errors. > > > > I found a similar problem in the archive, > > > > > https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-May/030025.html > > > > and I will follow the suggestion given. In the same time, does anybody > > know what is going wrong? > > > > Thank you very much! > > > > Sincerely, > > Ye > > > > > > ___ > > 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 > gr...@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.
Re: [Freesurfer] Missing ribbon.mgz file
Hi Ye, one of the programs expects that recon-all will be run all the way through instead of in parts. You will need to download a new version of mri_segstats from 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 Copy the file appropriate for your architecture to $FREESURFER_HOME/bin/mri_segstats doug On 07/02/2013 11:31 AM, ye tian wrote: > Dear freesurfers, > > Recon-all -s subject -autorecon2 returns the following error messages > > *mri_segstats will not calculate Supratentorial due to missing > ribbon.mgz file* > > mghRead(Path_to_subject/mri/*ribbon.mgz, -1)*: could not open file. > > Prior to autorecon2, I did recon-all -s subject -autorecon1, which > completed without errors. > > I found a similar problem in the archive, > > https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-May/030025.html > > and I will follow the suggestion given. In the same time, does anybody > know what is going wrong? > > Thank you very much! > > Sincerely, > Ye > > > ___ > 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 gr...@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] Missing ribbon.mgz file
Dear freesurfers, Recon-all -s subject -autorecon2 returns the following error messages *mri_segstats will not calculate Supratentorial due to missing ribbon.mgz file* mghRead(Path_to_subject/mri/*ribbon.mgz, -1)*: could not open file. Prior to autorecon2, I did recon-all -s subject -autorecon1, which completed without errors. I found a similar problem in the archive, https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-May/030025.html and I will follow the suggestion given. In the same time, does anybody know what is going wrong? Thank you very much! Sincerely, Ye ___ 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.
