Dear FSL experts,
Hello, I am posting the message once again, because I did not add some specific information.
I am trying to reconstruct the network from fiber tracking for DWI data.
I tried to register AAL atlas to individual native DWI space, but I figured out, it did not work perfectly.
So, I looked up several studies, and I met this conclusion:
1. T1-weighted image of each participant were firstly registered with their corresponding b = 0 image with affine or rigid body transformation.
2. the individual transformed T1* were registered to ICBM 152 T1 template in MNI.
3. inversed transformation parameter of each individual was applied to the AAL atlas to generate corresponding AAL regions in individual space.
Still, I am confusing on these steps; What I have understood so far is that
For 1. I have to register T1 data to dwi data ( nodif_brain.nii.gz, I belive) with flirt rigid body transformation.
For 2. With the above result, do non-linear registration to MNI T1 template in fsl bin.
For 3. ** This part is the most confusing one** use conver_xfm? to inverse whatever the param (probably *.mat file?) matrix, and apply it to AAL.nii.gz . Then transform it into native dwi space? Is this right?
Here is the bash command.
"""""
fname="${filename%.*}"
flirt -ref ${fname}_brain.nii.gz -in ${fname}_T1_orthogonal_brain_o_0.2.nii.gz -out ${fname}_T1todwi -omat ${fname}_T1todwi.mat -dof 6 -interp nearestneighbour
flirt -ref ${fname}_brain.nii.gz -in ${fname}_T1_orthogonal_brain_o_0.2.nii.gz -out ${fname}_T1todwi -applyxfm -init ${fname}_T1todwi.mat -out ${fname}_T1todwi_secondstep
flirt -ref $FSLDIR/data/standard/MNI152_T1_2mm_brain.nii.gz -in ${fname}_T1_orthogonal_brain_o_0.2.nii.gz -omat ${fname}_T1toMNI_affine.mat -interp nearestneighbour -dof 12
convert_xfm -omat ${fname}_MNItoT1_affine.mat -inverse ${fname}_T1toMNI_affine.mat
convert_xfm -omat ${fname}_MNItodwi_affine.mat -concat ${fname}_T1todwi.mat ${fname}_MNItoT1_affine.mat
flirt -in $cd ~/Documents/AAL2.nii.gz -ref ${fname}_brain.nii.gz -applyxfm -init ${fname}_MNItodwi_affine.mat -out ${fname}_AAL2toDWI.nii.gz -interp nearestneighbour -dof 12
"""""
+ I figured out AAL2 to DWI data does not perfectly register to my pre-processed 4D DWI data.
I am trying to do fiber tracking using deterministic tractography, and I really need your advice for further analysis.
Please give any comment on the bash script that I wrote.
Thank you in advance!
Sincerely,
Jean
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