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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@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. <dgr...@mgh.harvard.edu>
Subject: Re: [Freesurfer] Native volume to fs_average surface
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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
UK
Email: wells...@cardiff.ac.uk<mailto:wells...@cardiff.ac.uk>
Tel: 02920 879628
Web: Cardiff University
webpage<https://secure-web.cisco.com/1qNnVMUW-8a5g4kTCtKPEMvj0UwWQIdLND6XxJYbo4tDRipAKXuBUEBzgbZAP1lXMvaGia1qv4CVwhkpRSr6ze4btwYQWsPBXF9172QqzGbk-8zQ8POJMgfKLhoYlqEds__JwDF_zG9f289CNkX2fwdjVf2qNi7QMjGLvtmebXhTGvNlN4WJkHUjtrSuyeMHZKWiMMJ1rwH7gWnQc2Y1zV4Ipk5calhxSDe-3lSfyhyox5MUZv07sNEQskJ1ytooBhoOwkKGxH3zfOhfy-ODiYw/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: wells...@caerdydd.ac.uk<mailto:wells...@caerdydd.ac.uk>
Ffôn: 02920 879628
________________________________
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Fischl, Bruce
<bfis...@mgh.harvard.edu<mailto:bfis...@mgh.harvard.edu>>
Sent: Monday, April 19, 2021 5:06 PM
To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto: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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@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<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Native volume to fs_average surface
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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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Fischl, Bruce
<bfis...@mgh.harvard.edu<mailto:bfis...@mgh.harvard.edu>>
Sent: Monday, April 19, 2021 4:38 PM
To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>;
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@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<mailto:freesurfer@nmr.mgh.harvard.edu>>;
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Native volume to fs_average surface
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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
UK
Email: wells...@cardiff.ac.uk<mailto:wells...@cardiff.ac.uk>
Tel: 02920 879628
Web: Cardiff University
webpage<https://secure-web.cisco.com/1bACs9vZqLoF5os7vcJuO0_f0kS4gSCJq05ArUeI0a4WM7TACY5Bi5-4o0Z1P9vg-R9hHtfVn0kHqfjakmQWLVviO56JcAhbqfdDHfVgqUoowcUZdMnKbDiWym5n7aohtT0eIJ_YKvb6tbgUiQ2_VIK0d6leE7H3_yb0KMo1Em8suKcTBd0e5LKqNn8wiD6_hDSTVmDI3Xy7fgew7EUELef31qMj7CN_FpPUrRm22hHs/https%3A%2F%2Feur03.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsecure-web.cisco.com%252F1HVx_q4IeeU6MUK4bR-lwLecxoGjiTE9AkdIITGOuVqzhFz25f21HB_KD_xox0aiLKUrU36AMRc_NHZsd0lynv4xOUHF4n8Nqk-R2Fyb8R1B8SlNgpD9YezHNPbJfmr-HhqzOt46DluXDvnc350T3VAmL3GF2aCM8f702zSHHq7VROR17Fw72upBv2lGozjMUnKrFDZRzbwLvygRstUiP2CNLtGHka8B-acTJs5eiX4Kh5dOYOpbBVkmOQWMaSUiKV79Mvv7xxsAfFdsYMm8XZQ%252Fhttps%25253A%25252F%25252Feur03.safelinks.protection.outlook.com%25252F%25253Furl%25253Dhttps%2525253A%2525252F%2525252Fsecure-web.cisco.com%2525252F1WCYtSJa5SHotGCjKhAFSbD5jLy8xDueFAXlo_Vfk4WyJYhmxG18wqrEdh7CeV9mTj0Yb7tToqiZMK4BjCFizdNLYH-N2qvjFZBXjjzVuk0nOXKbFz3rLcfLKc77KhBxYw2suMHL8dMUCIZ0vIMWlmuRmZs1uINijmQi7svdcv2YBL1R8vQUNfhn7rQ5pLqWHn2eWdo7IanPd1h6fPoMcy5VcpnSbVH67JcPU0KQ3mtscRkf1cHQvi9AI1FyOEDOUp5V2kArCuIYHZhmkJvixJg%2525252Fhttps%252525253A%252525252F%252525252Fwww.cardiff.ac.uk%252525252Fpeople%252525252Fresearch-students%252525252Fview%252525252F974214-%252526data%25253D04%2525257C01%2525257CWellsMT1%25252540cardiff.ac.uk%2525257Cb8abee9390df48accada08d903496350%2525257Cbdb74b3095684856bdbf06759778fcbc%2525257C1%2525257C0%2525257C637544436006545496%2525257CUnknown%2525257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%2525253D%2525257C1000%252526sdata%25253DOaU1PbV0V5yeoLqaLQ5DBX2eGjet9dQInUOOR8A9QJE%2525253D%252526reserved%25253D0%26data%3D04%257C01%257CWellsMT1%2540cardiff.ac.uk%257C59e06b89f3914fdc47aa08d9034d2246%257Cbdb74b3095684856bdbf06759778fcbc%257C1%257C0%257C637544452091926929%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C1000%26sdata%3D6JZcyVOioUM3z%252F9TYg7Um%252FmTWbuXIu6DoJHfbNwh4Uw%253D%26reserved%3D0>
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: wells...@caerdydd.ac.uk<mailto:wells...@caerdydd.ac.uk>
Ffôn: 02920 879628
________________________________
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>>
Sent: Monday, April 19, 2021 10:27 AM
To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>;
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@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.
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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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Mason Wells
<wells...@cardiff.ac.uk<mailto:wells...@cardiff.ac.uk>>
Reply-To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Monday, April 19, 2021 at 4:23 AM
To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>,
"freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>"
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@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
UK
Email: wells...@cardiff.ac.uk<mailto:wells...@cardiff.ac.uk>
Tel: 02920 879628
Web: Cardiff University
webpage<https://secure-web.cisco.com/1Th7qZAvtg1NYOKAuxxyIaTmybR9dvbKmLr6iR7Knx6MpZ-WBohkDNHuA65JzDw75July-QsPf9l2RP48hEDGeHe53TTRPqZhCsSo9LoBbDJImVNrMGtAFdmDLhuGF1FFq4oenCW6fweIugPfg0YGFEKLl2do8Rocq1hViMsrk7XbgSlmShLHqUhB1rafvQZ4TSn7fkkz7K49GKisski8-1lzYadMzjTwRMEA8QwI36A/https%3A%2F%2Feur03.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsecure-web.cisco.com%252F1sHhRKnFtuWs0rLBliQpGmjSnmESqtv2qfhjIibytHvKkqdFk1PgJL4P_fKVQIyqaw6BwGBPqmaSZSF_0lQfrkX4nXiK1hDgt7JKgRkMMpzTJKvZKX1TnIhO17YbN9I0jWrWxInKxMeu5s92YGT2yhzQPvEiKVGyihRNuH07_6oR8KWlWABRgGw8W_os2PaKhSmFOpD75jNwBfr7Cv6_kaRA0WUpU5Nvgf9ZcsngXYeU%252Fhttps%25253A%25252F%25252Feur03.safelinks.protection.outlook.com%25252F%25253Furl%25253Dhttps%2525253A%2525252F%2525252Fsecure-web.cisco.com%2525252F18O020vXZIBYv3rUYS23vBvT7-YRSZBgjnRI_go1CHmqQMbwh6GID35oDZggTwSjB6Md_DuRp_nDCUkFRY-6c2orqtuwJGTRqttD3iAJ4pIxBGTRvzKvN59twE41VodR9ytmOrr8ZVoQgxtGpIGoB2e1LasEF77yrdUTjNkVv84efTHknXLMql-W6MvdXCr9W42YpIqL1DcqdjzCV5jaeDDDa4MLTajbtTMlzupt-homHrknIJgWnc7qIEv2AF0Rg-G8YD4WdmdCROidFeaWpdw%2525252Fhttps%252525253A%252525252F%252525252Feur03.safelinks.protection.outlook.com%252525252F%252525253Furl%252525253Dhttps%25252525253A%25252525252F%25252525252Fsecure-web.cisco.com%25252525252F1qGEoQnnU3besQKg-GQwdKq-WtCCzi1b5tl-HNLywYRQ48GHFhy2hNJxQfxY9t4vTe7V1-y5Gueo1-GHgls6xg6bCuHa7_Jm97SAxD4oOE1UzEYgt7j1TAqX1ySqfIvn8RozeJRSp-IFzu55FlX2sxTiuLxLWu0P4qA860qMdGbRyktdbz7B6M46-kYle2bYvPS1QR9PQNiqacvoErgAfRjfCdCy4DMcmKR4oB9wflZvX6HelaCoJDegiTXtqTXGM6biEq93kMOwFQdAsjxQytA%25252525252Fhttps%2525252525253A%2525252525252F%2525252525252Fwww.cardiff.ac.uk%2525252525252Fpeople%2525252525252Fresearch-students%2525252525252Fview%2525252525252F974214-%2525252526data%252525253D04%25252525257C01%25252525257CWellsMT1%252525252540cardiff.ac.uk%25252525257Cfd9cfc7e176848522b9e08d9031561d5%25252525257Cbdb74b3095684856bdbf06759778fcbc%25252525257C1%25252525257C0%25252525257C637544212657118100%25252525257CUnknown%25252525257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%25252525253D%25252525257C2000%2525252526s>
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: wells...@caerdydd.ac.uk<mailto:wells...@caerdydd.ac.uk>
Ffôn: 02920 879628
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