> 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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