Dear community,
I have already posted in this forum a few days ago, but after trying new approaches, we came up with a different command-pipeline where we again end up in problems.
We are doing a DTI-tractography study with several participants and want to align our subject-images with the template we use (MNI152), from which we also got the ROIs we do the research on.
Our new approach is the following:
flirt -dof 6 -in T1w_brain -ref b0_unwarped_brain.nii -out T1w_in_b0.nii.gz -cost mutualinfo
flirt -dof 12 -in T1w_in_b0.nii.gz -ref MNI152_T1_1mm_brain.nii.gz -omat T1w_to_MNI152.txt -out T1w_in_MNI152_lin.nii.gz
fnirt --ref=MNI152_T1_1mm_brain.nii.gz --in=T1w_in_b0.nii.gz --aff=T1w_to_MNI152.txt --cout=warps_into_MNI_space --config=T1_2_MNI152_1mm
After this fnirt command, we get no image (i.e. an empty file), as before. But when adding --iout=warps_into_MNI_space, we get one, but the resolution is really bad - how can that be?
When then using the warps-file as warp-input for the invwarp-command, we get an error: "FnirtFileReader:: msg=FnirtFileReader: Displacement fields must contain 3 volumes"
[By the way: the point is, that we can't use a skullstripped image in flirt but not in fnirt, since we use our outputs from flirt in the fnirt command]
What would you suggest? Are we right in taking T1w_in_b0 (instead of T1w_in_MNI152_lin) as the fnirt-input? Is there anything we can adjust with the parameters?
Thank you very much in advance!
Greetings from Germany,
Marvin, Clinical Cognition Sciences, UK Aachen, Germany
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