Hi I have one last question. I just noticed that my images are in Philips format. Would you recommend to convert to DICOM anyway? Or should I used NIFTI?Thanks,Pablo
Date: Tue, 27 Aug 2013 12:31:09 -0400 From: fischl@nmr.mgh.harvard.edu To: pablonajt@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Talairach Failure Detection
yes, definitely. The dicoms are best On Tue, 27 Aug 2013, pablo najt wrote:
Thank you very much for your input. Yes, I did start with analyze format and also I have visually inspected the images. Almost all my scans consistently show an extended whole in the prefrontal area (with a few exception of some scans showing this in posterior locations). I am assuming the best is to start with either DICOM or NIFTI and avoid analyze format. Is this correct?
Best, Pablo
Date: Tue, 27 Aug 2013 12:08:22 -0400 From: fischl@nmr.mgh.harvard.edu To: pablonajt@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Talairach Failure Detection
Hi Pablo
have you visually inspected the talairach xform to see if it is indeed incorrect? What input format did you start with? Most of these occur because people start with analyze, which doesn't have the direction cosines, and so the data is oriented incorrectly
cheers Bruce
On Tue, 27 Aug 2013, pablo najt wrote:
Dear FS experts,I am contacting you to report an error after launching recon -all for one of my subjects (see below). I am using a macbook pro with snow leopard version 10.6.8.
I would greatly appreciate if you could advise me which step/s should I take to correct this. Thank you for your attention, Pablo
Error:-------------------------------------------------------------------------------------------------------------------------------
#@# Talairach Failure Detection Mon Aug 19 23:01:43 EDT 2013 /Users/pablonajt/subjects/tr5713/mri \n talairach_afd -T 0.005 -xfm transforms/talairach.xfm \n ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0554, pval=0.0034 < threshold=0.0050) Manual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check flag follows -all or -autorecon1 in the command string. See http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach Darwin Pablo-Najts-MacBook-Pro.local 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386
recon-all -s tr5713 exited with ERRORS at Mon Aug 19 23:01:43 EDT 2013
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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.