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: wells...@cardiff.ac.uk<mailto:wells...@cardiff.ac.uk> Tel: 02920 879628 Web: Cardiff University webpage<https://secure-web.cisco.com/1FTTrTtQRbeOtWNs5HyjPsiwT162LYl006QjNjCg_aaV0KLoBZzKLR2cmzvDQxYW27__1jQ28G0iude6UjvXG3pDVWcRASgGPG3DbQbPfeRzFR1n5K7Ey5CyLpExBgY4dTuwvw5jih4AQnTX6vNBDqw3Ii39l0YAJHg5MEdtjerHX0ID1HKfsp-2X21-Dgd_DKLRsERPLBozYamJ8GMycu9cxEsg0CC7kruXVFuwbemvK4nQZHwV5tCaQDSWq_3idANOvGEiMS1de1nkOJKbG8g/https%3A%2F%2Fwww.cardiff.ac.uk%2Fpeople%2Fresearch-students%2Fview%2F974214-><http://secure-web.cisco.com/18VmpV313p_QRRrLmv8w1LfywUP6fQgssL2USLvjLy3umQsTOyyfhtojocuvAVLkVEGsLX4LAGzS-BGfv1s4SBa4MXPuYW6MgDEv_0GZiV6uE7iYgQ-yyrXUzSSGP2FI154x67S5XCh1gusy6AfltF_ax4u4cWa6Q4NIIw0odBFh0rTg725Y3KyZH6A6T5V9A2cmIEwFuK3s60MzvApSCPn0MWSs06dJHw6WpcQJSzNp5x2Y0M1e5kJZnjf_DA6XvEVKBY9VhVZttJfHcVN9mCQ/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: wells...@caerdydd.ac.uk<mailto:wells...@caerdydd.ac.uk> Ffôn: 02920 879628 ________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgr...@mgh.harvard.edu> Sent: Monday, April 19, 2021 2:57 PM To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Native volume to fs_average surface External email to Cardiff University - Take care when replying/opening attachments or links. Nid ebost mewnol o Brifysgol Caerdydd yw hwn - Cymerwch ofal wrth ateb/agor atodiadau neu ddolenni. If you have the data in the native functional space, then just mri_vol2surf --mov func.nii --hemi rh --reg reg.lta --trgsubject fsaverage --projfrac 0.5 --o rh.func.fsa.mgz On 4/19/2021 5:23 AM, Mason Wells wrote: External Email - Use Caution External Email - Use Caution Hi experts, I have some fMRI data that I have pre-processed in Feat. I want to resample a single subject's data to the fs_average surface but unsure of the most optimal way of doing this. At present I am warping the functional data to the MNI brain in the volume (using FSL's applywarp) and then resampling to fs_average using the following command. * mri_vol2surf --src filtered_func_MNI.nii --out filtered_func_surf.mgh --hemi rh --mni152reg My question is whether you think this is the most appropriate approach, and/or if there is way to move directly from native volume to fs_average surface without needing to go via MNI volume? Best wishes, Mason Mason T Wells, MSc PhD student School of Optometry and Vision Sciences & Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology Cardiff University Cardiff CF24 4HQ UK Email: wells...@cardiff.ac.uk<mailto:wells...@cardiff.ac.uk> Tel: 02920 879628 Web: Cardiff University webpage<https://secure-web.cisco.com/1Wkxi7Z70E6nZXn73eg4r66IHtr-XAAXqaaLBowkqIpKjKZenebYGxO7Texaa1P6_sf064wtdEmMKLfH_RHctTAiKFFTEckdwMmK2IaAEKcivzXITFteZnn0heaXgFX26Dts36MVqINvBR5wMRKEd4QSgK1F8SZ7iwiX08UGDPjZaOaTJyzfUZAAZ5-3oxzW_HMtfp-vTkSIkVpYmGLrmlugLicLN1iko0_F6dVxUitssSoFMaO_u1Mw8T8edUGz6BzDkegr94mcZqhpgJnU_eg/https%3A%2F%2Feur03.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsecure-web.cisco.com%252F1qGEoQnnU3besQKg-GQwdKq-WtCCzi1b5tl-HNLywYRQ48GHFhy2hNJxQfxY9t4vTe7V1-y5Gueo1-GHgls6xg6bCuHa7_Jm97SAxD4oOE1UzEYgt7j1TAqX1ySqfIvn8RozeJRSp-IFzu55FlX2sxTiuLxLWu0P4qA860qMdGbRyktdbz7B6M46-kYle2bYvPS1QR9PQNiqacvoErgAfRjfCdCy4DMcmKR4oB9wflZvX6HelaCoJDegiTXtqTXGM6biEq93kMOwFQdAsjxQytA%252Fhttps%25253A%25252F%25252Fwww.cardiff.ac.uk%25252Fpeople%25252Fresearch-students%25252Fview%25252F974214-%26data%3D04%257C01%257CWellsMT1%2540cardiff.ac.uk%257C3e5eb8ed6cfe42c21b7508d9033b59be%257Cbdb74b3095684856bdbf06759778fcbc%257C1%257C0%257C637544375715976304%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C1000%26sdata%3Dl739czeaTwikG2uw2x8bgtNfCCgfOrHt60gX5UsBj9I%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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://secure-web.cisco.com/1inKs6mkATk9l4A-1W4d1Qq75G9FVsDrr19kxb1PUwo3SJIzasjo5UqdO_zNla1MmfqmTW_UjyxKjaOzcgZ-34cmvBcj-twVDSjDeUdBMnfIQA6czUZ5Vr_q9mGbNXn_7mToecEWmYfGSE0PVRFfLnVUVqGvRB7EW657aXy9TDyUJo9XvcUdcs7MblDtwa3r9WFUz603xcRDAppL0KZfMto5GjYgrHa9MOoSsZp1ifyQghWl8Qe_fVmhvGeTsI71kHS0jbxKE43ugLOnZAXm14Q/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer<https://secure-web.cisco.com/1wnuFqExz9oizFYNN4VUj5zSJLDdFGvq87TlIHW-O3mOxhKLDjX87tReMlXtt06gH7Yxdv6ctVEgF1yDC9G5C2URvrn7pQooiPAd8slazhi4qgVWOjLrTvjACn6r9SlpSmc9PQvIXMwZwFBezzdvbdBVdewIMV2XWXXbOeszS2ZPwdFlSb15ilHsGqff4fMZW14kB7MfSKeFdJJ_XtPBcCS0-Uv-gk5CC4ZXwjLcKpsLKZ4Er1zwbl9eV9c_30Z1rLi23_1ibx2F564tlgnu9Dw/https%3A%2F%2Feur03.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsecure-web.cisco.com%252F1inKs6mkATk9l4A-1W4d1Qq75G9FVsDrr19kxb1PUwo3SJIzasjo5UqdO_zNla1MmfqmTW_UjyxKjaOzcgZ-34cmvBcj-twVDSjDeUdBMnfIQA6czUZ5Vr_q9mGbNXn_7mToecEWmYfGSE0PVRFfLnVUVqGvRB7EW657aXy9TDyUJo9XvcUdcs7MblDtwa3r9WFUz603xcRDAppL0KZfMto5GjYgrHa9MOoSsZp1ifyQghWl8Qe_fVmhvGeTsI71kHS0jbxKE43ugLOnZAXm14Q%252Fhttps%25253A%25252F%25252Fmail.nmr.mgh.harvard.edu%25252Fmailman%25252Flistinfo%25252Ffreesurfer%26data%3D04%257C01%257CWellsMT1%2540cardiff.ac.uk%257C3e5eb8ed6cfe42c21b7508d9033b59be%257Cbdb74b3095684856bdbf06759778fcbc%257C1%257C0%257C637544375715986305%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C1000%26sdata%3Dv6obWxRfZ55cJVTpyt8DfEsAbQRF89D7BLF0H7diuuk%253D%26reserved%3D0>
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