Bruce, I have visually checked the transforms and they do indeed seem incorrect. The images are stretched. I have attached the talairach.xfm for one of the images that failed and one that worked.
Thanks for all your help, Crystal On 1/13/13 3:08 PM, "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> wrote: >can you cc the list? Have you visualized the transform to see if it is >indeed incorrect? > >On Sun, 13 Jan 2013, Franklin, Crystal G wrote: > >> I used mri_convert to create the 001.mgz file. In freeview the >>directions appear correct. >> >> Thanks, >> Crystal >> -----Original Message----- >> From: Bruce Fischl <fis...@nmr.mgh.harvard.edu> >> Date: Sun, 13 Jan 2013 09:02:16 >> To: Franklin, Crystal G<frankl...@uthscsa.edu> >> Cc: Freesurfer@nmr.mgh.harvard.edu<Freesurfer@nmr.mgh.harvard.edu> >> Subject: Re: [Freesurfer] Freesurfer fails >> >> Hi Crystal >> >> how did you create the 001.mgz? When you view it in freeview does >> freeview have the correct directions in the anatomy (i.e. I/S, A/P and >> L/R)? >> >> cheers >> Bruce >> On Sat, 12 Jan 2013, Franklin, Crystal G wrote: >> >>> Freesurfer, >>> >>> I have been running a group of subjects through recon-all and some of >>>the >>> subjects are failing at the very beginning of the process and I am not >>>sure >>> why. The images look fine, but I keep getting the following error: >>> >>> #@# Talairach Failure Detection Fri Dec 7 10:54:57 CST 2012 >>> /Applications/freesurfer/subjects/PHY002/mri >>> \n talairach_afd -T 0.005 -xfm transforms/talairach.xfm \n >>> ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm >>> ***FAILED*** (p=0.0013, pval=0.0000 < threshold=0.0050) >>> INFO: Attempting MINC mritotal to perform Talairach align >>> >>> Do you know what could be causing this? >>> >>> I read that you can include the command ?notal ?check to skip this >>>test, but how >>> will this effect my data? If I run this command on the subjects that >>> failed and combine their results with the subjects that worked will my >>>group >>> results be effected? >>> >>> Any help would be appreciated. I have attached one of the log files >>>for a >>> subject that failed. >>> >>> Thanks, >>> Crystal >>> >>> >> >> >> 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. >> >> >>
failed_talairach.xfm
Description: failed_talairach.xfm
talairach.xfm
Description: talairach.xfm
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