Hello,
I just started working with fsl and I have a question regarding
co-registration.
I have a T2 MRI of a patient (pat_t2) and I would like to get the tensor
matrix at certain points. As I do not have a DWI from the same patient I
would like to use the JHU-MNI-SS DTI atlas.
From this atlas I have the tensor image (JHU_MNI_SS.d) which contains 6
image volumes of the tensor matrix, a co-registered T2 MRI
(JHU_MNI_SS_T2) and a co-registered T1 MRI (JHU_MNI_SS_T1).
I have tried to co-register pat_T2 as input to JHU-MNI-SS_T2 as
reference, so that pat_T2 is registered with the JHU_MNI_SS.d. I used
the following commands.
- bet pat_T2 pat_T2_brain -f 0.35
- bet JHU_MNI_SS_T2 JHU_MNI_SS_T2_brain -f 0.35
- flirt -in pat_T2_brain -ref JHU_MNI_SS_T2_brain -dof 12 -cost corratio
-out flirted_pat_T2 -omat pat_T2_to_JHU_T2.mat
After this I wanted to use fnirt as well but I am not sure if this is
the correct way and about the additional parameters to use.
The flirt registration needs to be improved.
1) Could you describe me how I can find the best registration? So far I
followed the inter-subject registration at “registration practical” on
the fsl web site
(http://www.fmrib.ox.ac.uk/fslcourse/lectures/practicals/reg/index.html).
2) How can I find the certain points (to read the tensor) in the pat_t2
image after my co-registration, especially if I have to do a non-linear
registration?
3) Is there another/better way to get the tensor values out of the
DTI-atlas (JHU_MNI_SS.d) at certain points in the pat_t2 image?
Thank you for your help.
Julia
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