Re: [Freesurfer] Surface-based smoothing of EPI data

That will work; it may be clearer to use mris_fwhm, eg, mris_fwhm --smooth-only --s sub-0006 --hemi lh --fwhm 5 --cortex --i input --o output

On 11/26/2021 6:48 AM, Mason Wells wrote:

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Hi Experts,

This question may have been addressed elsewhereon the list, but I can’t find a response.

I want to smooth BOLD data on the surface. First, I pre-processed the data in FEAT with no smoothing applied. Then I registered the filtered_func data to the anatomical using bbregister. I check the registration matrix looks good by running this command (using example_func as the reference):

• tkregisterfv --mov example_func.nii.gz --reg junk.dat --lta reg/freesurfer/anat2exf.register.dat --surfs

I then resampled my data with mri_vol2surf using the following command:

• mri_vol2surf --src filtered_func_data.nii.gz --out lh_func_native.mgh --srcreg reg/freesurfer/anat2exf.register.dat --hemi lh --projfrac 0.5 --out_type mgh

I then want to smooth this data on the surface. I assume it would be best to run mri_surf2surf and set the target and source subject as the same? Such as this command:

• mri_surf2surf --srcsubject sub-0006 --srcsurfreg lh.sphere.reg --trgsubject srcsubject--trgsurfreg sphere.reg --hemi lh --sval lh_func_native.mgh--tval lh_func_native_smoothed.mgz --mapmethod nnf --fwhm 5 --cortex

Please can someone on this list give me some advice on this? Are my command suitible and/or am I missing anything?

Best wishes, Mason

*Mason T Wells, MSc*

*PhD student*

School of Optometry and Vision Sciences

& Cardiff University Brain Research

Imaging Centre (CUBRIC), School of Psychology

Cardiff University

Cardiff

CF24 4HQ

UK

*/Email/*: WellsMT1@cardiff.ac.ukmailto:WellsMT1@cardiff.ac.uk

*/Tel/*: 02920 879628

*/Web/*: Cardiff University webpagehttps://secure-web.cisco.com/1u6t7awlKd_1Wa1q3V5QSyioa1OcxttJUnTK7KvQfyTiKmiVg9jTDdB2prTgVwu4ChmMoJRyRQg0biQClmgB-DxtRTLxOnkRmwAdfTvrTsGt8M2JZy6cYaer-nNp4lBC2CUlwhN0wH3TeHSnNzY7ybffoOnei5wLGmhFPfK7elwh_3voaHV0Mr6iX_tfGw2GIA2gBVT6f1tKAC5it_j9jXduR2hfnyvcvFTaSnlx3JJmk38ydwlyCH3Ee28BkMUEG6krlUUp2n009uhBkYGU9vWvYeX0OxkH3j3FVxSD13Ef5zckw-2vLYQtb8vFEQDFgU6r9q9zR6aAfXaYL4t7Uog/https%3A%2F%2Fwww.cardiff.ac.uk%2Fpeople%2Fresearch-students%2Fview%2F974214-

*Mason T Wells, MSc*

*Myfyriwr PhD*

Yr Ysgol Optometreg a Gwyddorau’r Golwg

& Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg

Prifysgol Caerdydd

Heol Maindy

Caerdydd

CF24 4HQ

DU

*/E-bost/*: WellsMT1@caerdydd.ac.ukmailto:WellsMT1@caerdydd.ac.uk

*/Ffôn/*: 02920 879628

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