Dear Naama,
sorry maybe I was not clear. I was suggesting flirting
your best target to the MNI152 instead of using the
"areg" affine registration that is done with the
standard TBSS protocol.
If it is working fine, then you should *first*
non-linearly register all your native FA images to the
best target (this has been created by your tbss_2_reg
step), *then* flirt all of them with the flirt matrix
created to register the best target to the MNI152...
The last step is then straightforward, but please
check first that you have indeed done this two-step
registration.
Best,
Gwenaelle
--- Naama Barnea-Goraly <[log in to unmask]> a écrit
:
>
>
>
> > Dear Gwenaelle and FSL experts,
> >
> > Thank you for your reply. Flirt does work well on
> my images and the
> > output looks good with the correct dimensions.
> However the path
> > from there is unfortunately still bumpy.
> > The problems that followed are probably due to my
> lack of
> > experience so sorry about the basic question:
> >
> > After having the "flirted" FA images (using
> parameters from the
> > transformation of the chosen target image to the
> MNI template), I
> > still need to merge them, create an All_FA image,
> a Mean_FA image
> > and the skeleton. I edited tbss_3 with the hope of
> doing that (see
> > below), but my mean image looks blurry (see
> attached). Could you
> > please tell me what I did wrong?
> >
> > Thanks,
> >
> > Naama
> >
> >
> > #!/bin/sh
> >
> > echo [`date`] [`hostname`] [`uname -a`] [`pwd`]
> [$0 $@] >> .tbsslog
> >
> >
> > echo "merging all upsampled FA images into single
> 4D image"
> > export FSLOUTPUTTYPE=NIFTI_GZ
> > ${FSLDIR}/bin/avwmerge -t ./all_FA
> `$FSLDIR/bin/imglob -oneperimage
> > *flirt_*`
> > #cd ../stats
> > $FSLDIR/bin/avwcpgeom MNI152 all_FA -d
> >
> > # create mean FA and skeleton and skeleton-mask
> > echo "creating mean FA"
> > ${FSLDIR}/bin/avwmaths all_FA -Tmean mean_FA
> > echo "skeletonising mean FA"
> > ${FSLDIR}/bin/tbss_skeleton -i mean_FA -o
> mean_FA_skeleton
> >
> > echo "now view mean_FA_skeleton to check whether
> the default
> > threshold of 2000 needs changing, when running:"
> > echo "tbss_4_prestats [threshold]"
> >
> >
> >
> >
> > >
> > On Jul 10, 2007, at 11:20 AM, Gwenaëlle DOUAUD
> wrote:
> >
> >> Dear Naama,
> >>
> >> sorry I have not followed all the emails about
> this
> >> transformation problem but it seems that
> everything is
> >> coming from the misregistration of your "best"
> target
> >> onto the MNI152. Have you identified this former
> and
> >> try to see if you can obtain something better
> just
> >> playing with Flirt and this target?
> >> Most of the time, Flirt happens to be much more
> robust
> >> than areg, the affine registration used to
> transform
> >> the best target into the MNI space in the TBSS
> >> protocol.
> >>
> >> Hope this helps,
> >> Gwenaelle
> >>
>
>
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