Still having issues with the subcortseg flag in v5.2.0 ... Trying to take a look at the source code, I did checkout from the cvs but it failed due to the following error:
cvs [checkout aborted]: Could not map memory to RCS archive /usr/fscvsroot/dev/distribution/average/cvs_avg35.tar.gz,v: Cannot allocate memory Any problems with the cvs server? Your help will be very much appreciated. Akio ---------- Forwarded message --------- From: Bruce Fischl <fis...@nmr.mgh.harvard.edu> Date: 2013/3/20 Subject: Re: [Freesurfer] subcortseg error - ?h.white surfaces not available Cc: Nick Schmansky <ni...@nmr.mgh.harvard.edu> I think something must be inconsistent with that flag. Can you use the workaround for now? On Wed, 20 Mar 2013, Akio Yamamoto wrote: Hi Bruce, > > After completing autorecon1 stage, I run: > > recon-all -s test -autorecon2 -autorecon3 > > and confirmed that it finished without errors, so I suspect mri_segstats > did not work correctly with the "-subcortseg" > flag in the new version 5.2.0. > > Here is the full command line where the error occurred: > > 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 --ctab > /usr/local/freesurfer/5.2.0/dist/ASegStatsLUT.txt --subject test > > > Now my questions are: > 1. Is there any change in mri_segstats from the previous version 5.1.0? > Or, is the "-subcortseg" flag no longer supported > in v5.2.0? > > 2. Any workaround for the use of "-sobcortseg" just after completing > autorecon1 in v5.2.0? > > > Thanks for your help. > Akio > > > 2013/3/19 A. Yamamoto <a.mtb...@gmail.com> > Hi Bruce, > > Here are command lines I used: > > recon-all -s test -i ./sample-001.mgz -i ./sample-002.mgz -autorecon1 > recon-all -s test -subcortseg > > > The error occurred in the final process, i.e. calculation of stats on the > automatic segmentation. > > Thanks, > Akio > > > 2013/3/19 Bruce Fischl <fis...@nmr.mgh.harvard.edu> > Hi Akio > > what was your full command line? > > cheers > Bruce > > On Mon, 18 Mar 2013, A. Yamamoto wrote: > > Hi, > > After upgrading to FreeSurfer 5.2.0, the command with > "-subcortseg" flag > exited with the following error. > > > MRISread(/usr/local/freesurfer/5.2.0/dist/subjects/test/surf/lh.white): > could not open file > > > I confirmed that the "-autorecon1" stage finished without > error. > In v5.1.0 it worked fine, so I'm wondering if there is any > change in > mri_segstats?? > > > FYI, I have attached the last part of recon-all.log file. > > Thanks for your help. > Akio > > > > > > 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. > > > > >
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