Ignoring question 2 - as instructed...
Question 1 - the script uses fsl_reg which calls FLIRT
and then FNIRT, so it is still necessary to run FLIRT
first, it is just hidden away in this case.
Question 3 - it depends on the images but our general
advice is to use betted images with FLIRT so that it
doesn't get distracted by non-brain material. However,
if you can't get a good brain extraction then don't do it
All the best,
On 9 Aug 2009, at 02:30, Mahinda Yogarajah wrote:
> Thank you for that pointer in the right direction. I wonder if I
> could ask
> a few other questions.
> I am trying to register segmented T1 GM maps in a subjects before
> and after
> development of a brain lesion to one another. I have done this by
> betting, followed by applying FAST. In trying to register the
> resulting GM
> images I have first tried to use FLIRT (with -inmasking of
> pathology) to
> derive a transformation matrix, before using FNIRT (again with
> My questions are :
> 1) Looking at the VBM scripts, in fslvbm_3_proc am I right in thinking
> native GM images are registered to a group specific template using
> FNIRT - if so why is there no need to use FLIRT first ?
> 2) When I try and use FLIRT (several options tried including affine/
> body models, weighting in mask, costfunction=normcorr,
> interp=trilinear) on
> my GM images I get strange results - images flipped, and sheared/
> zoomed. I
> get much better results using FLIRT with a command line that
> the VBM grey matter config file, but also with an inmask as above,
> and a
> native dilated subject refmask. I would be grateful for any advice
> here -
> eg is it critical to derive a FLIRT matrix before using FNIRT ?
> 3) Would it be better to derive the FLIRT matrix from betted,
> images, and then apply this to GM images ?