• bbregister --s sub-0006 --feat /media/HDD/ICA_SSD_files/GroupICA/PPT6_PreProc.feat/ --init-coreg
  

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Hi Doug,

I have the data both in its native functional space (e.g. filtered_func_data). I also run bbregister so have the transformation matrix to register it to the T1 (e.g. anat2exf.register.dat). Do you suggest running vol2surf on the filtered_func_data file? Also is reg.lta generated by FreeSurfer during recon-all or do I need to generate this file? I would like to end up with the filtered_func_data file on the fs_average surrface, which would require the file format to be .mgh to load this an overlay on Freeview, right? 

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.uk Tel: 02920 879628 Web: Cardiff University webpage

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.uk Ffôn: 02920 879628

---

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgreve@MGH.HARVARD.EDU>
Sent: Monday, April 19, 2021 2:57 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Native volume to fs_average surface

 

External email to Cardiff University - Take care when replying/opening attachments or links.

Nid ebost mewnol o Brifysgol Caerdydd yw hwn - Cymerwch ofal wrth ateb/agor atodiadau neu ddolenni.

If you have the data in the native functional space, then just
mri_vol2surf --mov func.nii --hemi rh --reg reg.lta --trgsubject fsaverage --projfrac 0.5 --o rh.func.fsa.mgz

On 4/19/2021 5:23 AM, Mason Wells wrote:

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Hi experts, 

I have some fMRI data that I have pre-processed in Feat. I want to resample a single subject's data to the fs_average surface but unsure of the most optimal way of doing this. At present I am warping the functional data to the MNI brain in the volume (using FSL's applywarp) and then resampling to fs_average using the following command.

• mri_vol2surf --src filtered_func_MNI.nii --out filtered_func_surf.mgh --hemi rh --mni152reg
  

My question is whether you think this is the most appropriate approach, and/or if there is way to move directly from native volume to fs_average surface without needing to go via MNI volume?

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.uk Tel: 02920 879628 Web: Cardiff University webpage

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.uk Ffôn: 02920 879628

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