Thank you. I will give it a try. Crystal
On 1/14/13 1:36 PM, "Nick Schmansky" <ni...@nmr.mgh.harvard.edu> wrote: >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
