Hi:
I have a skull stripped structural image. How may I begin the recon-all work flow from the segmentation stage? While many stages requires talairach coordinate, should I get the coordinates by running talairach with the original T1 image ( with skull )? however, that would require nuintensitycor to be run, will freesufer have trouble with the intensity during segmentation, because it's not intensity corrected images produced by freesurfer? I actually have made a few different attempts, but I always get a grey matter outline in the WM volume.
Also may I use some other software to give freesurfer a segmentation starting point, meaning feeding some segmented images into the wm directory? if so, how should the files be stored?
Thanks in advance,
Yuan-Fen Kuo Associate Imaging Processing Specialist Waisman Laboratory for Brain Imaging and Behavior University of Wisconsin - Madison