reg-feat2anat uses brain.mgz. But you'll have to give us more detail in order to evaluate the problem, "somewhat inaccurate" is not very informative. Please give cmd lines, versions, and log files. reg-feat2anat does use flirt, and it will print out the flirt cmd line. You can compare it to the one that you use. I assume you are using NIFTI?
doug
Bruce Fischl wrote:
I'll leave 2 for Doug. In 1. by segmentation do you mean the wm.mgz volume? Or the cortical parcellation? If the latter, which one (as we generate two by default).
cheers, Bruce
On Tue, 20 Jun 2006, Jeffrey Spielberg wrote:
Hi, I had a couple of questions regarding cortical/subcortical segmentation-
- In our cortical segmentation we keep getting what look to be
inaccurate segmentation of the rostral and caudal acc. It looks some of what should be labeled as one of those two areas is getting labelled corpus callosum or "unlabelled subcortical" instead, sometimes fairly large chunks. Does this indicate any problem earlier in the processing stream, and is there anything that can be done to prevent this? If not I saw that both tksurfer and tkmedit can be used to edit the segmentation, what would be the easiest way to do this?
- When registering a freesurfer anatomical to Feat output (using
reg-feat2anat) the registration seems to be somewhat inaccurate. Registering brainmask.mgz to our example_func using flirt has given us a better registration so far. Since reg-feat2anat seems to use flirt in its registration I was wondering what the difference might be resulting from. Does reg-feat2anat use T1.mgz as it's reference scan, and if so is there any way to have it use brainmask instead, as that seems to give better results?
Thanks, Jeff
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