Dear Doug,
As I mentioned in a previous email, I'm currently working with T1 DICOM files from the Clinical PACS System that I'd like to pull into the freesurfer stream to get cortical thickness. I've unpacked the data, converting the DICOM files to mgz format, and successfully ran the first recon-all command: "recon-all -i <input> -s <subject> -force". I then proceeded to run the "recon-all -autorecon-all -s <subject>" command on my subject, but the command terminated about 5 minutes in and I received the following error message:
#-------------------------------------------- #@# Talairach Failure Detection Mon Aug 20 13:53:21 EDT 2012 /autofs/cluster/roffman/users/Stable5_PerRun/Subject2/mri
talairach_afd -T 0.005 -xfm transforms/talairach.xfm
ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) Linux compute-0-35 2.6.32-220.23.1.el6.x86_64 #1 SMP Mon Jun 18 18:58:52 BST 2012 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s Subject2 exited with ERRORS at Mon Aug 20 13:53:21 EDT 2012
I tried viewing the talairach.xfm file in tkregister2, as I saw someone else who received the same error message was instructed to do, but no image would load (in the coronal and horizontal views the screen remained black and had one thin strip of grey in the center; the sagittal view brought up a blank white screen).
We know that our data is intact because Dr. Roffman is able to view images of this subject on his computer using the mi2b2 software, so do you think it is possible that somewhere earlier, either in the recon or the dcmunpack stages, there was an error with the data that wasn't recognized until doing the talairach transformation?
Also, something else I noticed when looking at our subject's data, the talairach.xfm and talairach.auto.xfm files are different, even though for all other subjects I've run recons on they are the same -- could this be a contributing factor?
I'm unsure how to proceed with the unpacking since I'm currently unable to perform any edits to the talairach registration to try and fix the error, so any suggestions would be very helpful and greatly appreciated!
Thanks, Alex