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 > _______________________________________________ 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.
