what format is your input data in? On Mon, 3 May 2010, Ilana Hairston wrote:
> I have also been getting error messages, after Talairach correction using > tkregister2 > > *...@# Talairach Failure Detection Mon May 3 09:57:40 EDT 2010 > /usr/local/freesurfer/subjects/FS060828cr/mri > > talairach_afd -T 0.005 -xfm transforms/talairach.xfm > > talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.6064, > pval=0.2817 >= threshold=0.0050) > > awk -f /usr/local/freesurfer/bin/extract_talairach_avi_QA.awk > /usr/local/freesurfer/subjects/FS060828cr/mri/transforms/talairach_avi.log > > TalAviQA: 0.93168 > z-score: -10 > ERROR: Talairach QA check failed! > z-score = -10 <= -6 = threshold > Manual Talairach alignment may be necessary, or > include the -notal-check flag to skip this test, > making sure the -notal-check flag follows -all > or -autorecon1 in the command string. > See http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach > Linux venus.mbni.med.umich.edu 2.6.18-128.1.10.el5 #1 SMP Thu May 7 10:35:59 > EDT 2009 x86_64 x86_64 x86_64 GNU/Linux > > recon-all exited with ERRORS at Mon May 3 09:57:40 EDT 2010* > > > On 3 May 2010 10:44, Janani Dhinakaran <janinthe...@gmail.com> wrote: > >> Hello experts, >> >> I've been having some trouble with the talairach during recon. I followed >> previous instructions and checked the rawavg image and found that it was in >> wrongly oriented. >> The sagittal picture was appearing under coronal but upsidedown, the >> coronal picture was sideways in the transverse section and the transverse >> was in the sagital section. I wonder if there is a place where I can send >> the data for someone to see and tell me how exaclty to flip the orientation >> of it to suit FreeSurfer. >> >> I would also like to know whether there is a shorter way of processing the >> data for only mri-stats without running recon-all for all the subjects' data >> we have. >> >> Thank you >> >> Jan >> >> _______________________________________________ >> 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. >> >> > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
