It worked!!!!
Once again thank you, Crystal
On 1/14/13 1:36 PM, "Nick Schmansky" nicks@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" 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 >> >> > > > 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. > > >
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