On 06/04/2018 04:01 AM, zuxfoucault Wong wrote:
>
>
> Hi Freesurfer experts,
>
> I am trying to resample the cerebellum atlas
> Buckner2011_17Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz
> to fmriprep output volume
> ${sub}_task-rest_bold_space-MNI152NLin2009cAsym_brainmask.nii.gz. I
> was wondering if the following 3 procedures are equivalent (if not
> what’s the difference?)?
>
> 1.
> mri_vol2vol --mov
> ${FREESURFER_HOME}/average/Buckner_JNeurophysiol11_MNI152/Buckner2011_17Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz
> --s ${sub} --targ
> ${project_path}/fmriprep/${sub}/func/${sub}_task-rest_bold_space-MNI152NLin2009cAsym_brainmask.nii.gz
> --o
> ${output_file_path}/Buckner2011_17Networks_MNI152NLin2009cAsym_brainmask.nii.gz
> --nearest
This uses the identity matrix as the registration matrix.
>
> 2.
> mri_vol2vol --mov
> ${project_path}/fmriprep/${sub}/func/${sub}_task-rest_bold_space-MNI152NLin2009cAsym_brainmask.nii.gz
> --s ${sub} --targ
> ${FREESURFER_HOME}/average/Buckner_JNeurophysiol11_MNI152/Buckner2011_17Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz
> --o
> ${output_file_path}/Buckner2011_17Networks_MNI152NLin2009cAsym_brainmask.nii.gz
> --nearest --inv
Probably the same as #1.
>
> 3.
> mri_vol2vol --mov
> ${FREESURFER_HOME}/average/Buckner_JNeurophysiol11_MNI152/Buckner2011_17Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz
> --s ${sub} --reg register.dat --o
> ${output_file_path}/Buckner2011_17Networks_MNI152NLin2009cAsym_brainmask.nii.gz
> --nearest
> where register.dat was generated by the following:
> bbregister --s ${sub} --mov
> ${FREESURFER_HOME}/average/Buckner_JNeurophysiol11_MNI152/Buckner2011_17Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz
> --int
> ${project_path}/fmriprep/${sub}/func/${sub}_task-rest_bold_space-MNI152NLin2009cAsym_brainmask.nii.gz
> --init-coreg --reg register.dat --t2
This is probably the one you want.
>
> Thank you for your time!
>
> Regards,
> Foucault
>
>
>
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