Hi Mason

Pretty much all surfaces of a single subject/hemi have the same topology (number of vertices/faces/etc…), so if you map to any of them you map to all of them.

As for the syntax for doing this in one step I defer to Doug. Doing it in 2 steps I would use the white or pial surface to go vol->surf, then the sphere.reg to go surf->surf

Bruce

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Mason Wells
Sent: Monday, April 19, 2021 12:16 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>; Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu>
Subject: Re: [Freesurfer] Native volume to fs_average surface

External Email - Use Caution

Hi Bruce,

No problem. I tried to run vol2surf using the following command, but it doesn't run.

mri_vol2surf --mov filtered_func_data.nii.gz --hemi rh --reg /home/masontwells/Documents/freesurfer/subjects/sub-0006/surf/rh.sphere.reg --trgsubject fsaverage --projfrac 0.5 --o rh_func_fsa.mgh

I get the following error:

ltaReadRegisterDat: could not read /home/masontwells/Documents/freesurfer/subjects/sub-0006/surf/rh.sphere.reg

No such file or directory

Doug, am I missing something obvious here?

Thanks for all your help,

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

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

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 Fischl, Bruce <BFISCHL@MGH.HARVARD.EDU>
Sent: Monday, April 19, 2021 5:06 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Native volume to fs_average surface

Hi Mason

I should have read to the end of my inbox before replying – Doug is the expert in this so I would definitely follow his advise over mine. In general the native->average surface transform is stored in the ?h.sphere.reg files

Cheers

Bruce

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Mason Wells
Sent: Monday, April 19, 2021 11:50 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Native volume to fs_average surface

External Email - Use Caution

Hi Bruce,

Thanks for the reply. Would you agree this is the optimal way to move from native vol to fs_average? I am confident with moving to native surface. My current pipeline for this is as follows. Anything here stick out that you think I should change?

bbregister to register the native functional volume data to the T1

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

Resampling to the native surface using the following command using the transformation matrix generated by bbregister:

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

I am not sure how to move from native surface to group average surface since I do not generate an appropriate transformation matrix to move from native surface to average surface in my pipeline. Can you offer any advice on this?

Cheers,

Mason

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Fischl, Bruce <BFISCHL@mgh.harvard.edu>
Sent: Monday, April 19, 2021 4:38 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>; freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Native volume to fs_average surface

Hi Mason

Yes, you can use mri_vol2surf to go native vol->native surf, then mri_surf2surf to go native surf->group surf

Cheers

Bruce

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Mason Wells
Sent: Monday, April 19, 2021 5:45 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>; freesurfer-bounces@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Native volume to fs_average surface

External Email - Use Caution

HI Matt,

Thanks for the reply. Are you suggesting I go native volume > native surface > fs_average? If so, can you recommend the best can I go from native to group average surface?

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

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

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 Glasser, Matthew <glasserm@wustl.edu>
Sent: Monday, April 19, 2021 10:27 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>; freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@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.

External Email - Use Caution

You would do that through the subject’s own surface. It does not work very well to map data directly from the volume onto group average surfaces (see e.g. Coalson et al., 2018 PNAS).

Matt.

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Mason Wells <WellsMT1@cardiff.ac.uk>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Monday, April 19, 2021 at 4:23 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>, "freesurfer-bounces@nmr.mgh.harvard.edu" <freesurfer-bounces@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Native volume to fs_average surface

External Email - Use Caution

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

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

E-bost: WellsMT1@caerdydd.ac.uk

Ffôn: 02920 879628

The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.