does the orig.mgz show up properly in tkmedit? On Wed, 23 Feb 2011, Nick Schmansky wrote:
> add the flag -notal-check to the end of recon-all command to skip the > check. > > if you can make your average using nifti format you're better off as > analyze doesnt retain orientation (l/r) info. > > you may have to manually register the brain following this: > http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach > > n. > > > On Wed, 2011-02-23 at 13:38 -0800, andrewkra...@ucla.edu wrote: >> Hello, >> >> I'm a complete newbie to FreeSurfer, so I appreciate any and all help >> you can provide. I am trying to use FreeSurfer to automatically create >> some masks of subcortical structures, but am having trouble getting >> the whole process started. >> >> When I run "recon-all -autorecon1 -noskullstrip -s FAD" (where FAD is >> my subject name) it quits with the error >> >> "ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm >> ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050)" >> >> >> I am trying to do this to a skull-stripped brain originally in Analyze >> format (there are no DICOMs since it's actually an average of many >> skull-stripped scans), to which I've already registered all of the >> scans I want to study. I used mri_convert to convert the .img file >> into a .mgz file, but compared to the bert example, the background >> (non-brain area) is a light gray instead of black. I don't know if >> this is where the error is occuring, and if it is, how to correct it. >> If it helps, the scan I'm trying to create masks from has been >> registered to the ICBM brain template. >> >> Let me know what other information you need and thanks for the help, >> -- Andrew >> _______________________________________________ >> 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 > > > _______________________________________________ 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.
