Thanks Mark! This is something I don't understand about SIENAX: Why does the BET2 result look so bad in the report but perfectly fine in FSLview?

This result was obtained already with the "Bias field and neck cleanup" option in BET2:

http://cns.bu.edu/~tren/sienax/extract.html

Tren

On Wed, Nov 30, 2011 at 5:16 PM, Mark Jenkinson <[log in to unmask]> wrote:
Dear Tren,

The brain extraction results here are terrible.
You really need to fix them before anything else will work.
Since you have an enormous amount of neck in your images,
I suggest you crop them with fslroi before doing anything else.

All the best,
Mark


On 30 Nov 2011, at 22:35, Tren Huang wrote:

Dear FSL experts,

I've applied fslreorient2std to my original structure images before any processing. Although in FSLView the orientation labels are correct and consistent between the structure images before and after FLIRT, the FLIRT results are reported with the wrong/original orientation by SIENAX:

http://cns.bu.edu/~tren/sienax/      (A modified SIENAX report)

I wonder how to fix this problem and if it's OK to proceed with further functional analysis?

Thanks!
Tren