Hi Noam,

noam Schneck wrote:

Hi,

I am trying to use reg-feat2anat to register my Feat analyses to anatomical images and running into a number of problems.

1. When I check the registration of the mean_func to the anatomical in

tkregister2 it looks fine. But when I overlay the fsl statmaps onto the anatomical brain they extend outside of boundaries of the anatomical brain.

Need more detail. What command are you using to visualize?

2. Also, before using reg-feat2anat. I was trying to do the

EPI_2_structural registration in FLIRT with the fsl.mat produced by BBR. When I try this the registered image is rotated 90 degrees from the original image. Why does that happen?

More detail needed. What program did you run? What visualization tool? This will align the anatomical in the conformed space to the EPI, so make sure you're using the right anatomical.

3. I also noticed that if I look at the header information for an

image in fslhd and mri_info the orientations are flipped. If the fslhd orientation is RAS it will be LPI in mri_info. Could this be related to what is happening in question (2)?

Need more detail. What images are you looking at?

In general, you have to tell us specifically what you are doing. It's going to be very hard to help with vague descriptions. doug

Best, Noam

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