Hi,
I'm afraid there was no attachment here (as the list does not accept anything except very small attachments, so you need to host images on an external website and send a link to it).
In terms of your steps, they are mainly fine. The major issue is that you do not use a configuration file in the call to FNIRT. You should definitely use a configuration file, and assuming that your 3D image is a T1-weighted image then you should use the $FSLDIR/etc/flirtsch/T1_2_MNI152_2mm.cnf
In addition, the 4th and 5th steps (convertwarp and applywarp) are unnecessary as you could directly output what you needed from the 3rd step (using -interp nearestneighbour) and I'm assuming that aal2mni and BA2mni are the same thing (and one it is a typo).
If you are not correcting for EPI distortions in any way then the registration is unlikely to be perfect and you should incorporate a fieldmap or phase-encode-reversed acquisitions into your protocol (or use them if you have already acquired them) in order to improve the registration.
I hope this helps.
All the best,
Mark
On 12 Oct 2013, at 15:09, Yan tang <[log in to unmask]> wrote:
> I used FSL to start fiber tracking of our DTI data. But when I use AAL template to find the some regions in DTI native space, I meet some problem. My program was as following:( 3D: subject's structural imaging; b0:subject's b0 in DTI; aal: AAL template ;ch2bet: AAL template' structural imaging)
>
> bet 3D b3D -f 0.3
>
> bet b0 nodif_brain -f 0.3 -m
>
> flirt -ref MNI152_T1_1mm_brain -in ch2bet -dof 7 -omat aal2mni.mat -out ch2_FSL -searchrx -180 180 -searchry -180 180 -searchrz -180 180
>
> convertwarp -m aal2mni.mat -r MNI152_T1_1mm_brain -o aal2mni
>
> applywarp --ref=MNI152_T1_1mm_brain --in=aal --warp=BA2mni --out=aal_FSL --interp=nn
>
> flirt -ref b3D -in nodif_brain -dof 7 -omat dti2str.mat -o dti2str -searchrx -180 180 -searchry -180 180 -searchrz -180 180
>
> flirt -ref MNI152_T1_1mm_brain -in b3D -omat affine_transf.mat -o affine_transf -searchrx -180 180 -searchry -180 180 -searchrz -180 180
>
> fnirt --ref=MNI152_T1_1mm_brain --in=b3D --aff=affine_transf.mat --cout=nonlinear_transf --iout=nonlinear_180
>
> convertwarp -o dti2mni_warp -r MNI152_T1_1mm_brain -m dti2str.mat -w nonlinear_transf
>
> invwarp -w dti2mni_warp -o mni2dti_warp -r nodif_brain
>
> applywarp --ref=nodif_brain --in=aal_FSL --warp=mni2dti_warp --out=aal_dti --interp=nn
>
>
>
>
> The result is in attachment. We will find that this registration is not good. For example, the MCC is on the top of the actual position. How can I revise my program?
>
> Pls tell me if you have any confusion of my questions. Look forward to your reply. Thanks a lot.
>
>
> Sincerely,
>
>
> Tangyan
|