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Thanks Douglas!
I also got replies from the author of fmriprep. Post his reply as the following link for future reference. https://neurostars.org/t/resampling-cerebellum-atlas-to-fmriprep-outcome/177...
Regards, Foucault
On Tue, Jun 5, 2018 at 6:29 AM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
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?)?
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.
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.
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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