please tell Anna that she indeed needs to reorient her images so that in fslview she would have the coronal view on the top left corner, axial view bottom left and sagittal view top right.
She can do that with the command fslswapdim.
--- En date de : Mer 4.3.09, Julian Henty <[log in to unmask]> a écrit :
> De: Julian Henty <[log in to unmask]>
> Objet: [FSL] FSLVBM image input
> À: [log in to unmask]
> Date: Mercredi 4 Mars 2009, 15h42
> ----- Original Message -----
> From: Anna Barnes
> To: Julian Henty
> Sent: Wednesday, March 04, 2009 1:38 PM
> Subject: please forward to FSL list for me and change
> subject heading to: FSLVBM image input
> Dear FSL users,
> I have just started using the FSLVBM tools and I need some
> clarification regarding image inputs. I've used
> fsl_vbm_bet1 -N to do the first level of processing on my
> MPRAGE images but on inspecting the results I find that the
> *_struc_cut.nii images have the LH side of the face removed
> and lots of neck remaining and the *_struc_brain.nii still
> having lots of neck left although most of the skull has been
> stripped. I assume that the first *struc_cut.nii step is
> suppose to remove most of the neck. The MPRAGE images are
> collected in sagittal orientation and FSLview displays them
> with all the correct orientation labels (A,P,S,I,L,R). Do I
> need to re-slice images into transaxial orientation before
> using the VBM scripts?
> Anna Barnes, PhD
> Research Associate (+441223 764676)
> Brain Mapping Unit (Sir William Hardy Bldg.)
> Dept. of Psychiatry.
> c/o Experimental Psychology
> University of Cambridge.
> Downing Site, Downing St.
> Cambridge, CB2 3EB