Crystal, I can replicate the failure you are seeing, and the problem is one that is fixed for the upcoming v5.2. It is described here:
https://surfer.nmr.mgh.harvard.edu/fswiki/TalFailV5.1 the first solution described should fix your problem. Nick On Mon, 2013-01-14 at 18:49 +0000, Franklin, Crystal G wrote: > > On 1/14/13 11:38 AM, "Franklin, Crystal G" <frankl...@uthscsa.edu> wrote: > > >I put the data on your ftp site in the folder called > >crystal_failed_talairach.tar. > > > >Thanks, > >Crystal > > > >On 1/14/13 9:31 AM, "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> wrote: > > > >>Hi Crystal > >> > >>we'll need the image volume also > >> > >>cheers > >>Bruce > >>On Mon, 14 Jan 2013, Franklin, Crystal G > >>wrote: > >> > >>> 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. > >>>>> > >>>>> > >>>>> > >>> > >>> > > > > > _______________________________________________ > 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
