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: wells...@cardiff.ac.uk<mailto:wells...@cardiff.ac.uk> Tel: 02920 879628 Web: Cardiff University webpage<https://secure-web.cisco.com/1QOYE7sZ5xjMi8AhHU9-TxeQOpoANZCHYIqIr41Lo2g2hhFf0IrxyB4KLkJNT3co26HFSXrOs146p8KI4J17qr_7NDGrIiiX0CC_El__4sMirG-N5Uu_Hq9USZv2OZc4PcPSagorXRR0ZbQbrx6jeNhTtJ_wBApEopGPIAYdeE7G8Afq-F7wVdMyK5p-qXa-fy4dhiGPk56cTmmDJuzCw3k4ii3o3VPEukl-6tPbiED_ceLfLVVz3OnKCzodMgJT_NZmnG5sP7kuFSxwDSJHlYQ/https%3A%2F%2Fwww.cardiff.ac.uk%2Fpeople%2Fresearch-students%2Fview%2F974214-><http://secure-web.cisco.com/1GUKoxYUP5Px7pVVEWS9Ni-ySmQ7y7ajTpj3KKBw5xMWenTVFfTNfqGSPK9BMJCuPwCciqDagkpFOesJQeyqPvSXRNjfgErQy312H_bHZeLxa9KlULq4BM8heVDt--zc1jt4u1mo-BTgLLbkQghDJpw1AkUetekO3eHjHglrmzbWujPkbl2yq8lRAuNRuge0knlMaQzojpssSHThoR_mPeGMTtWqtmYUnLJmCFG35_HeMn_XtqLTLz638DbBO5W69OihCapRwqLGn3gKKMvl_WQ/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: 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: wells...@cardiff.ac.uk<mailto:wells...@cardiff.ac.uk> Tel: 02920 879628 Web: Cardiff University webpage<https://secure-web.cisco.com/12JLw82TJoZfb6NTCxmKi4el1kNNVjiQmSDGPr0xmHNUH6u2wszxofXFE0jN32_GGi2TPIKnzih-Xaz8W8i9WIRUUSMJf3Wwv5lyUsYMzHecbnH2UZC1MbBQdUIw3H1AYcjYZpphg4Q_FUxSH-WhMH2PhOQcKuupMPAu3yEvdJbCDEFQtX2n4y5mumtXZCIKPGoJ4TAGEvS6jnOv4l1bQXB-mLf9amKE7JNj7_Ag_ldQkzve50X8XdnAoFp68ZdEybV4ODyRZur_zjuDF3CFElQ/https%3A%2F%2Feur03.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsecure-web.cisco.com%252F1FTTrTtQRbeOtWNs5HyjPsiwT162LYl006QjNjCg_aaV0KLoBZzKLR2cmzvDQxYW27__1jQ28G0iude6UjvXG3pDVWcRASgGPG3DbQbPfeRzFR1n5K7Ey5CyLpExBgY4dTuwvw5jih4AQnTX6vNBDqw3Ii39l0YAJHg5MEdtjerHX0ID1HKfsp-2X21-Dgd_DKLRsERPLBozYamJ8GMycu9cxEsg0CC7kruXVFuwbemvK4nQZHwV5tCaQDSWq_3idANOvGEiMS1de1nkOJKbG8g%252Fhttps%25253A%25252F%25252Fwww.cardiff.ac.uk%25252Fpeople%25252Fresearch-students%25252Fview%25252F974214-%26data%3D04%257C01%257CWellsMT1%2540cardiff.ac.uk%257C216ff6189ef043f3d90b08d9040598c4%257Cbdb74b3095684856bdbf06759778fcbc%257C1%257C0%257C637545244385194883%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C1000%26sdata%3DGtSxOWY7wH9q3U7I16kF%252F29gRwW9LBUCqhYAUmvbqeE%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 Douglas N. Greve <dgr...@mgh.harvard.edu><mailto:dgr...@mgh.harvard.edu> Sent: Monday, April 19, 2021 2:57 PM To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> <freesurfer@nmr.mgh.harvard.edu><mailto: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 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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> 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