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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.ukmailto:WellsMT1@cardiff.ac.uk
Tel: 02920 879628
Web: Cardiff University webpagehttps://secure-web.cisco.com/1KVQY_nwNJkNbz2ToDoEFcTs63TX7o8JLMxrm6fRYmu2Cmlub_8UrrYJjAsYf5Ic1day90_g6Zv3gWV-af2YrrSZEMFQJ50F9fpZax5F4xlj-fVt-14vNKE_IyO3RF8JVSgwqmA1Fj9I37NQCskBbmRglMxIPwTA7t92f5pV6FRIFJTlI_jeLNWuzgtk-nCrhmjg5UzVGcZlqllVigmKtjSk-AaBFoTEq4vVqT1sXkxYAIjKdsg2if9M9_Sa617q6FWJOYukBJ8iGnyJcrOZrcg/https%3A%2F%2Fwww.cardiff.ac.uk%2Fpeople%2Fresearch-students%2Fview%2F974214-http://secure-web.cisco.com/1Jr5c4Sna3e5IepK8m-pymwNI6Owxvbq-56MYF0gB9AP5_FHnQmQe7Hr6-nmfI4CQpqdGL5vL9uGyjBLI0MPrn3FFhJxtpnE9w4mm_jyYKe1lnp3zWGR2Ohx7qJ66LSLEfFEolkewFPy_n2QoBb5ZtBwOQLzUbDGcKooM7XTugBrX-JKQtpjYV6L5yYHziE6_gXXLAKjPQGCN21F6iDFcDU_e60_ZaxBmEypChNz1oedo9_rNRhPNmUe1VxOYh74WVYp3dkVHVooFgJeJFFv1Jg/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 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
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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.ukmailto:WellsMT1@cardiff.ac.uk
Tel: 02920 879628
Web: Cardiff University webpagehttps://secure-web.cisco.com/102EJ4ejZ6B8l7U7vBFeZSmKZ_MOE4fuua5M8UK2qEHTRdryTu1xakKTfhztkZQXtZGB5EeHHh8O--fTW6CQpqwzv6_z5j7adFSwW-JE3RNrxM-PNlvP482El1i7P3hfATQ7cdqXltcaxe4-1a8GTmaD88Q69QZjoNPVGWuM2V_qsYhuxA7FNCJwb9B3RRL_TMU1uYs454q52PhVGeC8GoHM4OoTnfH6KULL1D1Akfp6_cqYMPe8aso2ppQJWzD5BkmBk-LEwwnC9uQ7QFP3-sA/https%3A%2F%2Feur03.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsecure-web.cisco.com%252F1988ER71Tk1sEMq3ewXYyKSa_8SvDQTjPH73gsxlJhKKDA_uZyaXMe-2NfBpyFLzDtLD8K4hg-lJq3Z-VhPsAZFEn9-pFJOZb2pkvHtolr0_luJbP4dY_Bwg-xcQelSo1Y-rTjWkoVDcn6siDlFXszqrQRHk6BJSGZWGmeOWvfjN0N7zUrJPWOjym-ujmMGQyi3If12eb52wRiBa_Xfanm1LnM1iXfFERLvrk_9fGaKujHLNVHg46lGLBphhJOIa3-hs1Q6X210PkBrZg1I4phQ%252Fhttps%25253A%25252F%25252Fwww.cardiff.ac.uk%25252Fpeople%25252Fresearch-students%25252Fview%25252F974214-%26data%3D04%257C01%257CWellsMT1%2540cardiff.ac.uk%257C1e45c9237aba4d83601008d908c8dbef%257Cbdb74b3095684856bdbf06759778fcbc%257C1%257C0%257C637550481099938224%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C2000%26sdata%3DaTxi30VZeXTrKIq0xEzAGqjZ5f7WBVjjZj9G9jSpOwk%253D%26reserved%3D0https://secure-web.cisco.com/1Qed4fCpY42RPd4j8OpF4bbl74exjIfDhQkL4-EpK-qjfDqM6nohvIoKxd7yRNSxqwxj-lHfFzai9DdzU77IMDUF8MiWakvRSmTrllD2RXWvesmjzszHUsly1MTsQ-BjNTBgCu7WZsNHVxbDORR_6brGeJd9xCGrAbddrRLYV6raNGqFRVCs_A1UBpzMdC6Ra_vPbMZyJ1MuSRHC-mGWcUFNDcNs86UEByZ-f-mU6QvtPCAzB_mEzzEbHsXRCyqcD6Tj0CKWEH7HEa8siEXq_UA/https%3A%2F%2Feur03.safelinks.protection.outlook.com%2F%3Furl%3Dhttp%253A%252F%252Fsecure-web.cisco.com%252F1Qda9zCUrh8i8LVH0nZq6QLp3Zu8k36vNl8xyVpwJ0mxy9oAT3L02QM0KofUoRDjvzGwpdiYvQvcz20tdeoDGig8wgkOgaWJZfnkRyEo0dtWqhI3_RD3cvIacsQajso5csLEfiUYfA781BxC-cwfPPbEOEioQbt9MTjE6gcaCc6SipU1CHv5WMye5FKndZJGjWAKWCAAK349TMObcjlihqQhUcfBj06LHdTckaarv7PFaFZnwNt8iAv_DiiIo0RaMTo8l_B1dH1uj7-KUpzavrQ%252Fhttp%25253A%25252F%25252Fwww.cardiff.ac.uk%25252Fpeople%25252Fresearch-students%25252Fview%25252F482937-%26data%3D04%257C01%257CWellsMT1%2540cardiff.ac.uk%257C1e45c9237aba4d83601008d908c8dbef%257Cbdb74b3095684856bdbf06759778fcbc%257C1%257C0%257C637550481099948219%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C2000%26sdata%3D7B5UvLg90qThscnmXyHbb%252FN%252Bt%252Bz4JbDQjnk0lpw5Tz0%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: 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 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.ukmailto:WellsMT1@cardiff.ac.uk
Tel: 02920 879628
Web: Cardiff University webpagehttps://secure-web.cisco.com/1xiS-eVY92flBsL0qcAOrxKpVcPeQxLauuL8qfZ8U1M8LuzTV8sBi2e6DsxJFF6KE_MMLZIs8pCEIYQfOSUBuk3IuWlM_1uFi9p3i9ejZ7Fqai5JATbAGIBWkDzo4umLu0LjIDey6gcIXtZ3iXS65MCkdkdzv2o_UJdmgRh-vFDKpv83aONQ-vTy61s_bJifenAh2UN7_paiXmQUDi-PNUEfhpL8CtU_B23cVEwDrLw8/https%3A%2F%2Feur03.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsecure-web.cisco.com%252F1fOB1BY6uVXTnnAicnxQCXifoS6YdyxHxnyXgSJ5wu3FEVo6wmPcB6AjbMC-5CM16flXLFprxX_UA1GZcgbdbuAFTPwD_-62FQ9PTzS2o7607Nvh5N6bU2Rv2Zkx5cOdNcH3ir4imJ5lySB7B75WBhXHFU9ALFAvsrrVHbz0KGrT249H7d_w-o2rF8ElH2yzYN-m6aij-WqcfX9EiCaKiBRr83INnw3FOvbTip6GHpesgM4ADJsw-R0ukhmmPGngk1I6MCeEIF6zK1IuFGe-VjA%252Fhttps%25253A%25252F%25252Feur03.safelinks.protection.outlook.com%25252F%25253Furl%25253Dhttps%2525253A%2525252F%2525252Fsecure-web.cisco.com%2525252F1QOYE7sZ5xjMi8AhHU9-TxeQOpoANZCHYIqIr41Lo2g2hhFf0IrxyB4KLkJNT3co26HFSXrOs146p8KI4J17qr_7NDGrIiiX0CC_El__4sMirG-N5Uu_Hq9USZv2OZc4PcPSagorXRR0ZbQbrx6jeNhTtJ_wBApEopGPIAYdeE7G8Afq-F7wVdMyK5p-qXa-fy4dhiGPk56cTmmDJuzCw3k4ii3o3VPEukl-6tPbiED_ceLfLVVz3OnKCzodMgJT_NZmnG5sP7kuFSxwDSJHlYQ%2525252Fhttps%252525253A%252525252F%252525252Fwww.cardiff.ac.uk%252525252Fpeople%252525252Fresearch-students%252525252Fview%252525252F974214-%252526data%25253D04%2525257C01%2525257CWellsMT1%25252540cardiff.ac.uk%2525257C0e0be6943ccf4b86997508d908c728b5%2525257Cbdb74b3095684856bdbf06759778fcbc%2525257C1%2525257C0%2525257C637550473758081143%2525257CUnknown%2525257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%2525253D%2525257C2000%252526sdata%25253D7ogvjqHTcxi%2525252BbMhhUSEqVIrES6gL3uKmp4aq0dvTKmE%2525253D%252526reserved%25253D0%26data%3D04%257C01%257CWellsMT1%2540cardiff.ac.uk%257C1e45c9237aba4d83601008d908c8dbef%257Cbdb74b3095684856bdbf06759778fcbc%257C1%257C0%257C637550481099958217%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C2000%26sdata%3DCPod6n3TtNqjQq2YDAEQaFmfTWTOYxecIl4DPsG05DA%253D%26reserved%3D0https://secure-web.cisco.com/1X8sh6UqVarnnGL_m2vE7lAsyKqhKvDHCtXTJXv9S7yJcFZ97QN3MOu0k3dF3xOjM_FDUavZbwglE-WuDjGr0eU4AKWzU5-J2FrOUhgdmwh0-AR8VX1glTzHBYYaNMqQD1rP8pmxgnJ3OtQMBWFsiUodBAkDxCI-HskAKz7G_ww118A9jptW5IX_EivfVVnZjNEiCUGWtnd8J4V5e-GzorZyoXz2P_nqLP96SeRHyVhM/https%3A%2F%2Feur03.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsecure-web.cisco.com%252F1KPDLcSGPalBwYAaxFkJvRy3SWC--S0nbx6yDs9ofOQ6y8yOlK9Q200OXSQBeGPAzfR0cZqVCtm5F9UGlXnnNGkLIP8rR6DnliFFrwWmzaAyNoqD-C0Kwz-tN8bRFSecwsKgXiGaMUon70UuAubSt7-3Klx3mrvbNEaDPt8E_Tm1sWubs4q70JAj7KMtUaDBaOLiSz8X5UEOTr7hiAB9uz5TEZ3tM7GNjIIHiy01FcN-TlwX_i-0HLcFT2qgH5AHN8FDk3E_T0XHcrz_4Ue6Ezw%252Fhttps%25253A%25252F%25252Feur03.safelinks.protection.outlook.com%25252F%25253Furl%25253Dhttp%2525253A%2525252F%2525252Fsecure-web.cisco.com%2525252F1GUKoxYUP5Px7pVVEWS9Ni-ySmQ7y7ajTpj3KKBw5xMWenTVFfTNfqGSPK9BMJCuPwCciqDagkpFOesJQeyqPvSXRNjfgErQy312H_bHZeLxa9KlULq4BM8heVDt--zc1jt4u1mo-BTgLLbkQghDJpw1AkUetekO3eHjHglrmzbWujPkbl2yq8lRAuNRuge0knlMaQzojpssSHThoR_mPeGMTtWqtmYUnLJmCFG35_HeMn_XtqLTLz638DbBO5W69OihCapRwqLGn3gKKMvl_WQ%2525252Fhttp%252525253A%252525252F%252525252Fwww.cardiff.ac.uk%252525252Fpeople%252525252Fresearch-students%252525252Fview%252525252F482937-%252526data%25253D04%2525257C01%2525257CWellsMT1%25252540cardiff.ac.uk%2525257C0e0be6943ccf4b86997508d908c728b5%2525257Cbdb74b3095684856bdbf06759778fcbc%2525257C1%2525257C0%2525257C637550473758091132%2525257CUnknown%2525257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%2525253D%2525257C2000%252526sdata%25253DiPKf4J6Wlq04zPgpB7DK8R1C5%2525252BEuNuAx%2525252FQVu8Uci7Bs%2525253D%252526reserved%25253D0%26data%3D04%257C01%257CWellsMT1%2540cardiff.ac.uk%257C1e45c9237aba4d83601008d908c8dbef%257Cbdb74b3095684856bdbf06759778fcbc%257C1%257C0%257C637550481099968214%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C2000%26sdata%3DuixegSjqJUCilwdM4q1HltunhcNJoF8RDjNiqgS%252BmqQ%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: 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 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.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 Douglas N. Greve dgreve@MGH.HARVARD.EDUmailto:dgreve@MGH.HARVARD.EDU Sent: Monday, April 19, 2021 2:57 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto: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.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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