Freesurfer Experts,<br><br>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&#39;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.<br>
<br>All of the things that I&#39;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!<br>
<br>Chris McCarthy<br>