That is really surprising as we've registered these brains with no
Are you sure that they are not corrupted. Have you checked the brains
the BET output with FSLView? Have you done anything else to these
before running BET? In what way does it "fail"? Are you explicitly
the full path to the MNI152_T1_1mm_brain?
That is: $FSLDIR/data/standard/MNI152_T1_1mm_brain
And why have you only got 7 brains? There are many more in IBSR.
Are we talking about the same dataset?
Also, if they are clearly very different orientations (more than 90
then you should set the -searchrx -searchry and -searchrz options
You may find the GUI easier for this.
All the best,
On 14 Feb 2009, at 00:11, siamak wrote:
> Hi All,
> I am registering some IBSR dadaset images using flirt. First I bet
> the T1
> images like this:
> bet head_image brain_image
> then I use flirt as follows:
> flirt -in brain_image -ref MNI152_T1_1mm_brain -out flirted_image
> It failes to register for most of the images (6 from 7). Is there
> any comment?