Hi,
Unfortunately I can't see anything as you cannot send large
attachments to the list.
The first flirt call looks OK, but it assumes that your images
are stacked on the z-axis - is that the case? If not then it would
explain why things are failing.
The second flirt call really should have -dof 6 as part of it.
In order to check what is going wrong, you really should
look at the intermediate stages. For instance, what does
20_to_46 look like when overlayed (with FSLView) on 46_EP ?
And similarly for 46_to_MP overlayed on Pat_3T_32ch_MP_bet?
The final image, 20_EP_MNI is the combination of many
registrations, so doesn't really tell you which one failed.
Basically, everytime you run flirt, check what the -out image
looks like when overlayed on the -ref image. Only if this looks
good should you proceed.
Let me know what you find.
All the best,
Mark
On 1 May 2009, at 18:32, Patrick Bedard wrote:
> Hi Mark,
>
> Here's what I did, following these steps:
> file://localhost/homes/pbedard/Pat/fsl/doc/flirt/ztrans.html
>
> flirt -ref 46_EP.nii -in 20_EP.nii -schedule
> /homes/pbedard/Pat/fsl/etc/flirtsch/ztransonly.sch -out 20_to_46 -
> omat
> 20_to_46.mat
>
> flirt -ref Pat_3T_32ch_MP_bet.nii.gz -in 46_EP.nii -out 46_to_MP -omat
> 46_to_MP.mat
>
> flirt -ref /homes/pbedard/Pat/fsl/data/standard/
> MNI152_T1_1mm_brain.nii.gz
> -in Pat_3T_32ch_MP_bet.nii.gz -out MP_MNI -omat MP_to_MNI.mat
>
> convert_xfm -concat 46_to_MP.mat -omat 20_to_MP.mat 20_to_46.mat
> convert_xfm -concat MP_to_MNI.mat -omat 20_to_MNI.mat 20_to_MP.mat
>
> flirt -ref /homes/pbedard/Pat/fsl/data/standard/
> MNI152_T1_1mm_brain.nii.gz
> -in 20_EP.nii -applyxfm -init 20_to_MNI.mat -out 20_EP_MNI
>
> The 20_EP_MNI is completelly mis-aligned and rotated; it's even gard
> to
> really kbow in which way!
> I attached the anat overlaid by the 20_EP_MNI.
>
> Can you see what's not working right??
>
> Thanks!!
>
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