On 1/14/13 11:38 AM, "Franklin, Crystal G" FRANKLINC@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" fischl@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" fischl@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 fischl@nmr.mgh.harvard.edu Date: Sun, 13 Jan 2013 09:02:16 To: Franklin, Crystal GFRANKLINC@uthscsa.edu Cc: Freesurfer@nmr.mgh.harvard.eduFreesurfer@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
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