Yes, going thru the MNI volume will mess everything up with regard to the surface. Also, you should consider turning off any volume smoothing in feat and do surface smoothing once you have it on the surface.

On 5/3/2021 5:27 AM, Mason Wells wrote:

        External Email - Use Caution        

Hi Doug,

Sorry to email again RE this, but please could I get your advice on my pipeline below. The surface resampling of the filtered_func from native volume to fs_average looks very different to the output from moving from native volume > MNI volume > fs_average. I expected some differences as going via MNI volume will result in some signal loss, but I want to confirm I understood your advice properly. For example, is register.dat an appropriate matrix for moving directly from native volume to fs_average surface?

For reference, this is my interpretation of your earlier suggestion:

I register the filtered_func to the T1 using bbregister with this command:
  • bbregister --s sub-0006 --feat /media/HDD/ICA_SSD_files/GroupICA/PPT6_PreProc.feat/ --init-coreg

I then run the following command to sample the filtered_func to fsaverage surface:
  • mri_vol2surf --mov filtered_func_data.nii.gz --hemi lh --reg reg/freesurfer/register.dat --trgsubject fsaverage --projfrac 0.5 --o lh_func_fsa.mgz

Any advice would be much appreciated.

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

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Mason Wells <WellsMT1@cardiff.ac.uk>
Sent: Monday, April 26, 2021 4:32 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Cc: Douglas N. Greve <dgreve@MGH.HARVARD.EDU>
Subject: Re: [Freesurfer] Native volume to fs_average surface
 

        External Email - Use Caution        

Hi Doug,

If I understand you correctly. I register the filtered_func to the T1 using bbregister with this command:
  • bbregister --s sub-0006 --feat /media/HDD/ICA_SSD_files/GroupICA/PPT6_PreProc.feat/ --init-coreg

I then run the following command to sample the filtered_func to fsaverage surface:
  • mri_vol2surf --mov filtered_func_data.nii.gz --hemi lh --reg reg/freesurfer/register.dat --trgsubject fsaverage --projfrac 0.5 --o lh_func_fsa.mgz
Please could you let me know if you think this is correct?

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

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Mason Wells <WellsMT1@cardiff.ac.uk>
Sent: Monday, April 26, 2021 4:20 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Native volume to fs_average surface
 

        External Email - Use Caution        

Hi Doug,

Sorry for the slow reply to this. I am not sure I follow your suggestion. Are you suggesting I register the filtered_func to the T1 with bbregister which results in a reg.lta/dat file? How does one then use this transformation matrix to move from native space to fs_average space? 

Thanks in advance,
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

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgreve@MGH.HARVARD.EDU>
Sent: Tuesday, April 20, 2021 3:06 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Native volume to fs_average surface
 
use the filtered func data. reg.lta  the output of bbregister (might also be a .dat file). If the output is on fsaverage, then you can use nifit as output. FV will read mgh, mgz, nii, nii.gz, as well as dicom

On 4/19/2021 10:26 AM, Mason Wells wrote:

        External Email - Use Caution        

        External Email - Use Caution        

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:

        External Email - Use Caution        

        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

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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