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
