Hi Bruce, Thanks for your response. It's a bit of a pain to access the dicoms, but it's possible. The bigger problem now is that I can't get freeview to work. I type in freeview into the command line and receive the following error:
freeview.bin: error while loading shared libraries: libvtkverdict.so.5.6: cannot open shared object file: No such file or directory Forgive my lack of linux knowledge, but is there some software I failed to download? I searched for the error in the Mail Archive and the only entry is from April 7, 2011. The response to the query says something about glxgear. Is that something I should try to get freeview running? If so, how do I do that? As a side note, tksurfer and tkmedit seem to work fine. Jared On Dec 12, 2013, at 3:36 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > Hi Jared > > for the ones that run quickly and end, it's because you haven't told it to do > anything. The first couple of lines of the recon-all.log file give the > command line as: > > Thu Dec 5 14:00:18 MST 2013 > /mnt/NAS3/freesurfer/freesurfer//bin/recon-all > -i Time3_28908_s11038064-0005-00001-000001-01.nii -subject Time3_28908 > > this will just convert the nifti and create the subject dirs for Time3_28908. > You need to add "-all" at the end of the line, as you did in the other ones. > > For the one that failed the talairach it's hard to say. You are starting with > nifti - can you try it directly on the dicoms? Where did you get the nifti > from? If you bring the nifti input volume up in freeview does it show in the > correct orientation? That is, is what freeview thinks is anterior truly > anterior, etc....? > > cheers > Bruce > > > > > On Thu, 12 Dec 2013, JARED NIELSEN wrote: > >> Hi, >> >> I'm new to FreeSurfer and have been going through the tutorials, YouTube >> videos, and Mail Archive. I've run recon-all on a handful of scans with >> variable success. Some of the scans are processed after five or six hours >> without any problems, and the output looks good. Others are processed >> "without any errors" after a matter of minutes, and logically I don't see >> any output. Finally, others hit a hard error after a few minutes of >> processing during the talairach transformation step. I looked at the >> orig.mgz file (for the scan that failed at transformation step) through >> tkmedit, and it is a blank white rectangle. I don't see anything that >> resembles a head or brain. I've attached examples of each recon-all.log >> (i.e., good, bad, and bad_talairach). Any help would be greatly appreciated. >> >> Thanks, >> Jared >> > > > 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
