External Email - Use Caution
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
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
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
Thank you for your time!
Regards, Foucault
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
External Email - Use Caution
I found whether procedure 1 or 3 produced the misaligned result. Did I miss some steps? [image: bbregister_misalign.png]
Best, Foucault
On Tue, Jun 5, 2018 at 3:52 PM zuxfoucault Wong zuxfoucault@gmail.com wrote:
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
freesurfer@nmr.mgh.harvard.edu
-
Douglas N. Greve -
zuxfoucault Wong