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
UK
Email: WellsMT1@cardiff.ac.ukmailto:WellsMT1@cardiff.ac.uk
Tel: 02920 879628
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
________________________________ 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.
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
UK
Email: WellsMT1@cardiff.ac.ukmailto:WellsMT1@cardiff.ac.uk
Tel: 02920 879628
Web: Cardiff University webpagehttps://secure-web.cisco.com/1WCYtSJa5SHotGCjKhAFSbD5jLy8xDueFAXlo_Vfk4WyJYhmxG18wqrEdh7CeV9mTj0Yb7tToqiZMK4BjCFizdNLYH-N2qvjFZBXjjzVuk0nOXKbFz3rLcfLKc77KhBxYw2suMHL8dMUCIZ0vIMWlmuRmZs1uINijmQi7svdcv2YBL1R8vQUNfhn7rQ5pLqWHn2eWdo7IanPd1h6fPoMcy5VcpnSbVH67JcPU0KQ3mtscRkf1cHQvi9AI1FyOEDOUp5V2kArCuIYHZhmkJvixJg/https%3A%2F%2Fwww.cardiff.ac.uk%2Fpeople%2Fresearch-students%2Fview%2F974214-http://secure-web.cisco.com/1MNPrmQJR9550op3djBOU1j5o9nBXwXKoLLRfoEZxKWyKrZcnXvc64hHZ8exVRny1RTmTbBxUUS5D2zeVGIQAmD2iCr8LyGsx5e3Po_IU49GBDKveJKjTr7Kbi9Oafv1rzQcr64ymq4bFlwBR5MqeiybnHd-dn7bsu34l67IEIyEcPu57o5CCg8lMVnH9Z_4bCtTlXNMesg2vXtGa90_hpUu48Rkpig_V9i53Rg9bqQfpBJkswmheAqGZt8WGdDKiioznhkcXsN0aeobFZe6kEQ/http%3A%2F%2Fwww.cardiff.ac.uk%2Fpeople%2Fresearch-students%2Fview%2F482937-
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
________________________________ 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
UK
Email: WellsMT1@cardiff.ac.ukmailto:WellsMT1@cardiff.ac.uk
Tel: 02920 879628
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
________________________________
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.
External Email - Use Caution
What is most important is that you map to your individual’s surface (whether that is in subject’s physical space or MNI space doesn’t matter so much). If you are using FreeSurfer formatted data, others can suggest how to do this. With NIFTI/GIFTI/CIFTI, it can be accomplished with wb_command -volume-to-surface-mapping and wb_command -metric-resampling among other things (e.g. see https://secure-web.cisco.com/1_Cq1etkFEJqfTFb_02eCv_lWyZdh6vGfkdd5A81SPw-162...).
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 4:45 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 - 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
UK
Email: WellsMT1@cardiff.ac.ukmailto:WellsMT1@cardiff.ac.uk
Tel: 02920 879628
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
________________________________ 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
UK
Email: WellsMT1@cardiff.ac.ukmailto:WellsMT1@cardiff.ac.uk
Tel: 02920 879628
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
________________________________
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.
________________________________ 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.
External Email - Use Caution
I am using FreeSurfer formatted data, yes. I believe I am mapping to the individual surface correctly, but can I double check you agree?
I am running bbregister to register the functional data to the T1 which appears to do a good job:
* bbregister --s sub-0006 --feat /media/HDD/ICA_SSD_files/GroupICA/PPT6_PreProc.feat/ --init-coreg
I then resampling to the 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
If suggest a different route to do this, I would appreciate your advice.
And if anyone else on the list can offer some advice on how to move from native surface to fs_average surface that would be great. I assume it will be via mri_surf2surf, but unsure as to correct flags to use to do this correctly.
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/13Fq5E_xlSpLpEI-ckdTfTBYhm6b4RnZnitkQ2ciHOkrjCXI2Bgy6R_A7lKaLRe3XejBJgUJc9a1iavhFbROdZ2XVnggc4AN4L1yY7a1-TDImm-0sRbV_6N-WXx8ZaexE1UdVJOtUnXzR52oj1-6OBD0VhEnmYSg3igcAnpLncTfq2_JtbszZQhR66zmngg1hn3urUCaMd0H68Wp-_JCfVfs3unuss-unSZ2erGktSzLY8isswlN32Yq5AC675LkNrNmG9YjumKVYTw2YgYn17g/https%3A%2F%2Fwww.cardiff.ac.uk%2Fpeople%2Fresearch-students%2Fview%2F974214-http://secure-web.cisco.com/1YYrZsGXUp2z9OLBFxY_A8AyY4mgUNG05g6LNq6Ijrdu2beldTjcLWHeOCaaaZr-hcB2rWw-_eehlwYMKDev0B0expBSynU8xWPpR_yGQ5PcCEsAI52svGf1OuB6MLnN2V7nL5xYYnwGXuUfsUz3mW_cZgtGHrrmM-h7ki-kVC36MF3hGUS_ALhYpJ_DiJACYiy-fe-izZzENagkHVFP_dqh9nAnGBVhtxvCHUsP0GLton_TZJbsc-aeG1GvvvhJIB8RF5Fp_Kv4cxHBL2Kftwg/http%3A%2F%2Fwww.cardiff.ac.uk%2Fpeople%2Fresearch-students%2Fview%2F482937-
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
________________________________ 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 10:51 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 - Use Caution
What is most important is that you map to your individual’s surface (whether that is in subject’s physical space or MNI space doesn’t matter so much). If you are using FreeSurfer formatted data, others can suggest how to do this. With NIFTI/GIFTI/CIFTI, it can be accomplished with wb_command -volume-to-surface-mapping and wb_command -metric-resampling among other things (e.g. see MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1JkyRNDeyhQOlg46XxB1DXCPusiuym31oLp2ufoVM0b0rRQ...https://secure-web.cisco.com/1u_x2sJZo6utdstestn2GI3H87ayA3Df-ruBYv6lJlN6qQSaKBEy3oofWKNqmxy4s_ytLBRpNAjSenxuwPhtxJUFbqlFuZmwPDcNainMmhpjOGd4oCtqtGX9kcp2bLISBzeECNvU9jBhcxh7gupAPuVtzep_T02e27zamr69m5GJIXsNG-TdxXc5MjuD3xzFjd9pwUyqOyjx8B8LBtaXWP4HaW-fWj-u-ZhS1bu0CuWHDKO8ApMtPm7KycvW3UhzEYBSulXoYPvUzWWsQ_wLNQg/https%3A%2F%2Feur03.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsecure-web.cisco.com%252F1_Cq1etkFEJqfTFb_02eCv_lWyZdh6vGfkdd5A81SPw-162gbs9u3HNA1PnuI7IsLrhkGjH3RxADhe1uk6zpOS4uCtg9YOdXFh8Z0VVcD8z-PgaZzq3v-LlDwgk5DfFfrJE-OMomZ4ZIA9-Q8Ihk3gRZ0O4LWEOd6nvAZ3AdlWe0nxXANY2zKCNEgv_fUrnQq3PJEce8MeX5SdLB-FImrnAJX6gVvKh18gh6sVI9yzAfTF0TcJQ5eLy-JcnQzrOFcFPp4ssonrJT6Tcfqvk0m3w%252Fhttps%25253A%25252F%25252Fgithub.com%25252FWashington-University%25252FHCPpipelines%25252Fblob%25252Fmaster%25252FfMRISurface%25252Fscripts%25252FRibbonVolumeToSurfaceMapping.sh%26data%3D04%257C01%257CWellsMT1%2540cardiff.ac.uk%257C2bc096305d2e42b3a47208d90318b95e%257Cbdb74b3095684856bdbf06759778fcbc%257C1%257C0%257C637544227282580447%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C2000%26sdata%3DonZCSJ%252BqbbMwKvfa8vc8su1R8GtPpJOz3DGYrWoB7CU%253D%26reserved%3D0).
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 4:45 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 - 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
UK
Email: WellsMT1@cardiff.ac.ukmailto:WellsMT1@cardiff.ac.uk
Tel: 02920 879628
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
________________________________
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
UK
Email: WellsMT1@cardiff.ac.ukmailto:WellsMT1@cardiff.ac.uk
Tel: 02920 879628
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
________________________________
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.
________________________________
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.
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
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
UK
Email: WellsMT1@cardiff.ac.ukmailto:WellsMT1@cardiff.ac.uk
Tel: 02920 879628
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
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Glasser, Matthew <glasserm@wustl.edumailto:glasserm@wustl.edu> Sent: Monday, April 19, 2021 10:27 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu>; freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Mason Wells <WellsMT1@cardiff.ac.ukmailto:WellsMT1@cardiff.ac.uk> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Monday, April 19, 2021 at 4:23 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu>, "freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu" <freesurfer-bounces@nmr.mgh.harvard.edumailto: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
UK
Email: WellsMT1@cardiff.ac.ukmailto:WellsMT1@cardiff.ac.uk
Tel: 02920 879628
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
________________________________
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.
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
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
UK
Email: WellsMT1@cardiff.ac.ukmailto:WellsMT1@cardiff.ac.uk
Tel: 02920 879628
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
________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Glasser, Matthew <glasserm@wustl.edumailto:glasserm@wustl.edu> Sent: Monday, April 19, 2021 10:27 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu>; freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Mason Wells <WellsMT1@cardiff.ac.ukmailto:WellsMT1@cardiff.ac.uk> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Monday, April 19, 2021 at 4:23 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu>, "freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu" <freesurfer-bounces@nmr.mgh.harvard.edumailto: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
UK
Email: WellsMT1@cardiff.ac.ukmailto:WellsMT1@cardiff.ac.uk
Tel: 02920 879628
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
________________________________
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.
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
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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Fischl, Bruce <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> Sent: Monday, April 19, 2021 4:38 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu>; freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto: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.edumailto:freesurfer@nmr.mgh.harvard.edu>; freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Native volume to fs_average surface
External Email - Use Caution
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
UK
Email: WellsMT1@cardiff.ac.ukmailto:WellsMT1@cardiff.ac.uk
Tel: 02920 879628
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
________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Glasser, Matthew <glasserm@wustl.edumailto:glasserm@wustl.edu> Sent: Monday, April 19, 2021 10:27 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu>; freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Mason Wells <WellsMT1@cardiff.ac.ukmailto:WellsMT1@cardiff.ac.uk> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Monday, April 19, 2021 at 4:23 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu>, "freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu" <freesurfer-bounces@nmr.mgh.harvard.edumailto: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
UK
Email: WellsMT1@cardiff.ac.ukmailto:WellsMT1@cardiff.ac.uk
Tel: 02920 879628
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
________________________________
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.
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
UK
Email: WellsMT1@cardiff.ac.ukmailto:WellsMT1@cardiff.ac.uk
Tel: 02920 879628
Web: Cardiff University webpagehttps://secure-web.cisco.com/1qNnVMUW-8a5g4kTCtKPEMvj0UwWQIdLND6XxJYbo4tDRipAKXuBUEBzgbZAP1lXMvaGia1qv4CVwhkpRSr6ze4btwYQWsPBXF9172QqzGbk-8zQ8POJMgfKLhoYlqEds__JwDF_zG9f289CNkX2fwdjVf2qNi7QMjGLvtmebXhTGvNlN4WJkHUjtrSuyeMHZKWiMMJ1rwH7gWnQc2Y1zV4Ipk5calhxSDe-3lSfyhyox5MUZv07sNEQskJ1ytooBhoOwkKGxH3zfOhfy-ODiYw/https%3A%2F%2Fwww.cardiff.ac.uk%2Fpeople%2Fresearch-students%2Fview%2F974214-http://secure-web.cisco.com/1y8UZ2C2uSqjt0TjzAVmldKPHXnqooRGK8ahnM-ht-dU2oE-fj7RPRjIPjdORLzwmCDiAesxI4dhXnYtmWL5bXQZtnsMOW1F9213uhuaDMcALJdwjE_JPEhWzvW3VRF_Kt5Gag4yJGfSoyeG6Bq0pKzdiCCl3yLYYUM7K2qL75-93FduZWP9HGgi7YnZsnUW1wRNsP4FXoLS1SwQH9VoPw-Z34LcUEmps3MGiQI1WnjihxlVO46HAmKh_4CucLh9rMq3T7JfzZAjlTSCg7V9P0w/http%3A%2F%2Fwww.cardiff.ac.uk%2Fpeople%2Fresearch-students%2Fview%2F482937-
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
________________________________ 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
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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Fischl, Bruce <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> Sent: Monday, April 19, 2021 4:38 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu>; freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto: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.edumailto:freesurfer@nmr.mgh.harvard.edu>; freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Native volume to fs_average surface
External Email - Use Caution
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
UK
Email: WellsMT1@cardiff.ac.ukmailto:WellsMT1@cardiff.ac.uk
Tel: 02920 879628
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
________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Glasser, Matthew <glasserm@wustl.edumailto:glasserm@wustl.edu> Sent: Monday, April 19, 2021 10:27 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu>; freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto: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.
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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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Mason Wells <WellsMT1@cardiff.ac.ukmailto:WellsMT1@cardiff.ac.uk> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Monday, April 19, 2021 at 4:23 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu>, "freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu" <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> Subject: [Freesurfer] Native volume to fs_average surface
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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.ukmailto:WellsMT1@cardiff.ac.uk
Tel: 02920 879628
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
________________________________
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.
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
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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
UK
Email: WellsMT1@cardiff.ac.ukmailto:WellsMT1@cardiff.ac.uk
Tel: 02920 879628
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
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Fischl, Bruce <BFISCHL@MGH.HARVARD.EDUmailto:BFISCHL@MGH.HARVARD.EDU> Sent: Monday, April 19, 2021 5:06 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto: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.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Native volume to fs_average surface
External Email - Use Caution
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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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Fischl, Bruce <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> Sent: Monday, April 19, 2021 4:38 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu>; freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto: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.edumailto:freesurfer@nmr.mgh.harvard.edu>; freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Native volume to fs_average surface
External Email - Use Caution
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
UK
Email: WellsMT1@cardiff.ac.ukmailto:WellsMT1@cardiff.ac.uk
Tel: 02920 879628
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
________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Glasser, Matthew <glasserm@wustl.edumailto:glasserm@wustl.edu> Sent: Monday, April 19, 2021 10:27 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu>; freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Mason Wells <WellsMT1@cardiff.ac.ukmailto:WellsMT1@cardiff.ac.uk> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Monday, April 19, 2021 at 4:23 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu>, "freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu" <freesurfer-bounces@nmr.mgh.harvard.edumailto: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
UK
Email: WellsMT1@cardiff.ac.ukmailto:WellsMT1@cardiff.ac.uk
Tel: 02920 879628
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
________________________________
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.
External Email - Use Caution
Thanks Bruce.
Doug, can I get your advice on this? As I say, I currently do the following to get to native surface:
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
But unsure of how to get to fs_average surface from this surface, or the appropriate command and flags to move from native vol to fs_average surface.
Thanks again for your help
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/1FUoi0vInzLgwXl2UINKZG-YDWLtrIwOCAvqX1wwMUj_aaVSsei6eMbXppAYo9GC8zLVTncNUDYgfDBphiwwkJt2dwt_YPXggqEEmYhs-lWdhw3r3fmu3U5UlBPfgTYDwU_3ZntGTP2A0qZamtyEHCHpahDXwFT9cvC1QaVTqd5I3tiHVSNNB17Sf0T50YpekM20NEE6QKq8ni_ZzEMOoyk8OfBXUS6zzXwJT6I0IxinyepJ2LGXwBtlvkDopk0ppTVMCLv6Ydp0HrIqqkXEqow/https%3A%2F%2Fwww.cardiff.ac.uk%2Fpeople%2Fresearch-students%2Fview%2F974214-http://secure-web.cisco.com/15dLJaE5alCxElB09P-5AJhOovexmIe-32koQG4Zd00pcfa8kHg7g1Af62UV9hBhcEID90s4u6rSA77eE_GQwBERQ7co7iG9rV_KNJp0uOjGNpqP9k98_nxSZFOjxCK_BrcmiXZdHtE8a9Xm4sZwChRqhmaM-IAwkAK3i725Sco8p37ItS5AOBekhjcbjdBU4yS1ltrb4OvafE8Agq-wlc5LMcMsd64GnFlAl30BZH_j_Eon8wTDe-W4QboM01X_iVA_4oK-axiUAXnO6rZNuew/http%3A%2F%2Fwww.cardiff.ac.uk%2Fpeople%2Fresearch-students%2Fview%2F482937-
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
________________________________ 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 5:22 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
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
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
UK
Email: WellsMT1@cardiff.ac.ukmailto:WellsMT1@cardiff.ac.uk
Tel: 02920 879628
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
________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Fischl, Bruce <BFISCHL@MGH.HARVARD.EDUmailto:BFISCHL@MGH.HARVARD.EDU> Sent: Monday, April 19, 2021 5:06 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto: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.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Native volume to fs_average surface
External Email - Use Caution
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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Fischl, Bruce <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> Sent: Monday, April 19, 2021 4:38 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu>; freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto: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.edumailto:freesurfer@nmr.mgh.harvard.edu>; freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Native volume to fs_average surface
External Email - Use Caution
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
UK
Email: WellsMT1@cardiff.ac.ukmailto:WellsMT1@cardiff.ac.uk
Tel: 02920 879628
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
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From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Glasser, Matthew <glasserm@wustl.edumailto:glasserm@wustl.edu> Sent: Monday, April 19, 2021 10:27 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu>; freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Native volume to fs_average surface
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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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Mason Wells <WellsMT1@cardiff.ac.ukmailto:WellsMT1@cardiff.ac.uk> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Monday, April 19, 2021 at 4:23 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu>, "freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu" <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> Subject: [Freesurfer] Native volume to fs_average surface
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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.ukmailto:WellsMT1@cardiff.ac.uk
Tel: 02920 879628
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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freesurfer@nmr.mgh.harvard.edu
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Fischl, Bruce -
Glasser, Matthew -
Mason Wells