External Email - Use Caution I installed Freesurfer v.4.5 and tried to qcache this old data, but ran into an error (segmentation fault). I wondered if there were some settings or files I might be missing? (Or if I had old libraries that stopped FS from completing?)
I downloaded freesurfer-Linux-centos4_x86_64-stable-pub-v4.5.0-full.tar.gz (from https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/4.5.0/). A log file is located here-- https://www.dropbox.com/s/9c3d0kgbafqpgx3/P0008_000_01-FS_recon-all.log?dl=0 (Though the error output is a bit sparse). Additional suggestions to try? Thanks much! On Thu, Jun 14, 2018 at 12:47 PM Jamie Hanson <jamielarshan...@gmail.com> wrote: > > I tried that, but no luck. FS ran into issues with ?h.white.H and then > ?h.w-g.pct.mgh (maybe more errors). Is there a way to use qcache in 4.5? > Could I simply download and install v.4.5 ( > https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/4.5.0/) and go > from there? I couldn't find instructions for v.4.5, but would the syntax of > 'recon-all -s $sub -qcache' work? > > Thanks much! > > > On Wed, Jun 13, 2018 at 11:20 AM Douglas N. Greve <dgr...@mgh.harvard.edu> > wrote: > >> I have no idea how to make it work with data that old. You can "fool" it >> by copying or soft linking lh.curv to lh.white.K. You can probably get >> it to at least finish. >> >> >> On 06/06/2018 03:41 PM, Jamie Hanson wrote: >> > >> > External Email - Use Caution >> > >> > >> > Hello all, >> > >> > I was trying to run qcache on some previously processed Freesurfer >> > data from a colleague, but ran into some issues with missing files and >> > wondered how best to proceed. >> > >> > Details: >> > -The data was processed with (Freesurfer) v4.5.0 and I would ideally >> > like to not reprocess it with a newer version (to keep in concordance >> > with past published work, and also it's a large number of subjects, >> > n=800+). >> > -The qcache flag was not used with the data previously (to my >> > knowledge), so I was attempting to run this command: recon-all -s >> > $subj -qcache >> > -When I try that command, I get an error regarding a >> > missing lh.white.K file. >> > >> > I've uploaded the log file here: >> > https://www.dropbox.com/s/94mnsy7wrps5ce2/recon-all.log?dl=0 >> > >> > I wondered if it was possible to complete qcache with the data as is? >> > I searched on the list previously and saw one or two other folks had >> > run into this issues; I, however, didn't see a final solution to >> > things. Any thoughts or suggestions are greatly appreciated! Thanks >> much! >> > >> > Best, >> > Jamie. >> > >> > -- >> > Jamie Hanson >> > Assistant Professor, Psychology >> > Research Scientist, Learning Research and Development Center >> > University of Pittsburgh >> > Personal website: jamiehanson.org <http://jamiehanson.org> >> > >> > >> > >> > _______________________________________________ >> > Freesurfer mailing list >> > Freesurfer@nmr.mgh.harvard.edu >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> _______________________________________________ >> 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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