Good morning Neuroimaging Experts,
I am running CSD probabilistic tractography on the S900 release of the Human Connectome Project dataset. I am trying to convert my .tck files to MNI space, and to do this I followed @eloydelas instructions from 2016, which can be reviewed at this link: https://community.mrtrix.org/t/warping-tck-files-using-ants-warps/162. My ultimate goal is to do the following:
I have attached subject-space tractography and my failed MNI normalization to this post for your reference. They are named accordingly.
My pipleline is delineated as follows:
1. Create no-warp images in target space:
warpinit \
$FSLDIR/data/standard/MNI152_T1_2mm_brain.nii.gz \
no-warp-[].nii
2. Warp target images to subject space:
for s in ${subjects}
do
for n in 0 1 2
do
fnirt \
--ref=dtifit_output/DTI_FA.nii.gz \
--in=no-warp-${n}.nii \
--aff=standard2diff_${s}.mat \
--iout=warp-${n}_${s}.nii
done
done
3. Perform MNI normalisation on .tck images:
for s in ${subjects}
do
tcktransform \
ifod2_paths.tck \
warp-[]_${s}.nii \
ifod2_paths_mni.tck
done
4. Please note that I also tried redoing this process perfoming the following intermediary step in FSL:
for s in ${subjects}
do
for n in 0 1 2
do
fslorient \
-copysform2qform \
warp-${n}_${s}.nii
done
done
I would sincerely appreciate any advice this community may be able to offer!
Kind regards,
Linda
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