Freesurfer Experts,
I am having lots of success, and making progress, with FreeSurfer thus far. I have been able to load DICOMS into Slicer3 to reorient, and resample them, after using FSL to extract the brain. Loading these brains into FreeSurfer is straight forward, and I've run them through the entire process. However, I am still hoping to use brains that have been previously skull stripped but are unfortunately saved in analyze (.img, .hdr) format.
All of the things that I've tried have led to a talairach error, and the brain being incorrectly oriented when loaded in tkmedit. Using slicer3, however, I was able to load the .img file and put the brain in ACPC space using the ACPC registration module included. It still gives me a talaraich error, but if I run recon1 with -notalcheck, the process runs without error and the brain is correctly oriented in tkmedit. Is this data usable? If I run it with notalcheck will I be unable to use volumetric analysis reliably? Thanks for your help and patience!
Chris McCarthy