Dear Corinna,

I am not sure what is (or whether is) something wrong with your commands, but in any case I would be cautious of interpretation of results using such method, mainly from following reasons:

1.
mni152reg uses 12 DOF whole-brain registration. You cannot expect to get perfect alignment of subcortical regions using such crude transform. To obtain more precise transform, I would use either registration targeted specifically to subcortical regions (e.g. using first_flirt in FSL, which is, however, still affine only), or use mri_cvs_register.

2.
Due to no reasonable contrast within thalamus to allow to distinguish the nuclei using even state-of-the-art MR imaging, such registration-based atlas method would by necessity be a simple transfer of predefined atlas onto the subject space, with no information to guide the alignment within the thalamus itself (it would basically be a best-guiess of where these nuclei might be, with no scope for subject-specific refinement).

Antonin Skoch


Hi al, Just wondering if anyone has any suggestionsto my previous question
as to why the volume from mni152 space would be rotated, even though the
MNI152 to subject T1 alignment looks good?

As a recap, here are my commands:

 mni152reg --s ${subject} --1

tkregister2 --mov ${subj_dir}/mri/mni152.orig.mgz --targ
/usr/share/fsl/5.0/data/standard/MNI152_T1_1mm_brain.nii.gz --reg
${reg_file}

  mri_vol2vol --mov ${subj_dir}/mri/orig.mgz --targ
/home/Documents/thalamus/AtlasMNI152/left-vols-1mm/global.nii.gz --reg
${reg_file} --inv --o ${out_dir}/lh_global.nii.gz

tkmedit -f subject/mri/orig.mgz -aux ${out_dir}/lh_global.nii.gz -ov
${out_dir}/lh_global.nii.gz -fminmax .5 1

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