Dear experts, I am preparing seeds for a later tractography analysis in fsl (sorry about this). I am bit concerned about the location of my final seed regions and wanted to ask you if there is something wrong in my pipeline.
I first started using recon-all -subject HC015 -i HC015.nii.gz -all. Then used the following command to label my seeds (here the thalamus): mri_binarize --match 10 --i aparc+aseg.mgz --o left_thalamus.nii.gz Afterwards I used bbregister and mri_label2vol to map each label into diffusion space: bbregister --s HC001 --mov HC001/mri/b0_brain.nii.gz --reg HC001/mri/registration2b0.dat --dti --init-fsl mri_label2vol --seg left_thalamus.nii.gz --temp b0_brain.nii.gz --reg registration2b0.dat --o left_thalamus_dwi_seed.nii.gz If I now open this image in fslview, it corresponds not really with the thalamus (mricron works). I am concerned now using the images for probtrackx. I attach the thalamus image. Thanks a lot for your help Andre
left_thalamus_dwi_seed.nii.gz
Description: left_thalamus_dwi_seed.nii.gz
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