Dear whom it may concern,
I'm having trouble getting applywarp to correctly apply the prior conducted registrations to the functional scan. Here are the steps that I have conducted so far:
1) I have registered the T1 scan (t1.nii) to the MNI brain (mni_brain.nii) using FSL's flirt & fnirt. I used the code below. These steps have worked well.
flirt -in t1.nii -ref mni_brain.nii -dof 12 -out t1_linreg -omat t1_to_mni_lin.mat
fnirt --in=t1_linreg.nii.gz --aff=t1_to_mni_lin.mat --config=T1_2_MNI152_2mm.cnf --iout=t1_linreg_nonlinreg.nii.gz --cout=t1_to_mni_coef.nii.gz
2) Then, I registered the EPI scan (f01.nii) to the T1 (t1.nii) using the following code. This step also seemed to work well.
.
** FYI -- f01_stc_mc is the slice time corrected & motion corrected functional scan.
fslroi f01_stc_mc f01_stc_mc_firstvol 0 1
robustfov -i t1 -r t1_fov
bet t1_fov t1_fov_bet –f 0.4 –g -0.09 –R
flirt –in f01_stc_mc_firstvol –ref t1_fov_bet -omat f01_to_t1.mat –out f01_to_t1.nii.gz
3) Then, I tried to combine the transformations using applywarp (or apply the initial transformations to the functional scan).
applywarp --ref=mni_brain.nii.gz --in=f01_stc_mc.nii.gz --out try1.nii.gz --warp=t1_to_mni_coef.nii.gz --premat=t1_to_mni_lin.mat
I don’t really understand why applywarp did not work in this situation. Can you please advise? I can also include screenshots of the results in fsleyes if that would be helpful. I could not attach them to this message, since they exceeded the file size limit.
Thank you!
Yasmine Bassil
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