Hi Antonin,
Thank you for your input. I will give mri_cvs_register a try.
Best,
Corinna
On Mon, Apr 24, 2017 at 10:24 AM, Antonin Skoch <a...@ikem.cz> wrote:
> 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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