FSL and SPM99/SPM2 deal with the image orientations differently. If you work
with the most recent version of FSL and SPM5b, then you should find rather
more compatibility (I hope).
Best regards,
-John
On Wednesday 10 August 2005 16:24, Stephen J. Fromm wrote:
> On Wed, 10 Aug 2005 14:31:02 +0100, Anusha Sritharan
>
> <[log in to unmask]> wrote:
> >Hi
> >
> >I am not sure whether I should send this mail to spm or fsl or to both,
> >but decided on sending to spm first.
> >
> >I have a dti data set from which I have computed the FA maps using FSL-FDT
> >tool box. I am planning to do VBM type analysis on FA maps using SPM2.
> >
> >Here is my problem:
> >
> >The B0 and all other images used for FA calculation when displayed using
> >SPM2 have voxel size (-1.88 1.88 2.5). However, when I displayed FA map
> >and other related images(computed using fsl-fdt) the voxel size is (1.88
> >1.88 2.5) with left-right flipped (I checked this by looking at the global
> >shape of the images). But, when these images are displayed using fslview
> >they all looked very well matched, ie there is no L-R flipping in the FA
> >maps.
>
> I don't have a specific answer. But I do recall that when I used the FSL
> skull-stripping tool on Analyze images, the resulting image was left-right
> flipped when I viewed it in SPM2.
>
> Not sure whether the interpretation of the orientation of Analyze images
> are different between FSL and SPM2; I just dealt with it on an ad hoc
> basis (in my case, wrote a Perl script to change the sign on the x-pixel-
> size in the *.hdr file).
>
> >I am con-puzzeled by this. I need to do spatial normalsation of Fa maps
> >before perfomring the t-test comparison between groups and I am thinking
> >of flipping the FA maps using reorient in SPM2 so that it will be in same
> >L-R orientation as the templates.
> >
> >I look forward to hear from you all.
> >
> >Thanks in advance
> >
> >Anusha
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