External Email - Use Caution Great, thanks for this. Am I right in thinking that the only outputs from this command are COR-.info and COR-001 and that neither of these should have which hemisphere it was created from in their name? I also notice the examples on the wiki page have more inputs/arguments, I assume these are not needed for what I am trying to do? E.g. resample filtered_func to the surface using the anat2exf.register.dat file?
Thanks again, 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 Tel: 02920 879628 Web: Cardiff University webpage <https://www.cardiff.ac.uk/people/research-students/view/974214-> 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 Ffôn: 02920 879628 On 17/04/2020, 18:40, "Douglas N. Greve" <dgr...@mgh.harvard.edu> wrote: That looks good. The only thing to change is to specify the projection fraction for vol2surf to --projfrac 0.5 (so that it samples in the middle of the cortical ribbon rather than at the white/gray boundary) On 4/17/2020 1:36 PM, Mason Wells wrote: > External Email - Use Caution > > Hi, > > Can I just double check this seems correct to you experts? I am not 100% proficient in Freesurfer/FSL. > > I ran: > bregister --s S1 --feat Data/Feat2/LM/scans/Preprocessed_functionals/6_CMRRMB_run1_.feat/ > > Which seemed to give me what I needed, the white matter appears to be well aligned with the functional data when I ran: > tkregisterfv --mov / Data/Feat2/S1/scans/Preprocessed_functionals/6_CMRRMB_run1_.feat//example_func.nii.gz --reg Data/Feat2/S1/scans/Preprocessed_functionals/6_CMRRMB_run1_.feat//reg/freesurfer/anat2exf.register.dat --surfs > > Now I believe I need to resample this to the surface with mri_vol2surf. Is the command as simple as: > > mri_vol2surf --src /scans/Preprocessed_functionals/6_CMRRMB_run1_.feat/filtered_func_data.nii.gz --out /Preprocessed_functionals/ --srcreg /Preprocessed_functionals/6_CMRRMB_run1_.feat/reg/freesurfer/anat2exf.register.dat --hemi rh > > followed by the same command with lh instead for the other hemisphere? Or are the additional commands that you would recommend? > > Thanks for all your help. > Mason > > > > Mason T Wells, MSc > PhD student > School of Optometry and Vision Sciences > & Cardiff University Brain Research > Imaging Centre (CUBRIC), School of Psychology > Cardiff University > Cardiff > CF24 4HQ > UK > > Email: wells...@cardiff.ac.uk > Tel: 02920 879628 > Web: Cardiff University webpage <https://www.cardiff.ac.uk/people/research-students/view/974214-> > 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 > Ffôn: 02920 879628 > > > On 17/04/2020, 17:40, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of dgr...@mgh.harvard.edu> wrote: > > Yes, use the template.nii.gz as the registration target. A long time ago > we used to have some wrappers that would operate directly on feat > folders. Not sure if they still work but, check out > https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FFslFeatFreeSurfer&data=02%7C01%7CWellsMT1%40cardiff.ac.uk%7Cd1f3f081039a4d49340808d7e2f660e9%7Cbdb74b3095684856bdbf06759778fcbc%7C1%7C0%7C637227420124409244&sdata=lKy%2B8H9gAxvdLv8vKuqLp3kZ4FdMPlsRgx7AYmVqmvw%3D&reserved=0 > > On 4/17/2020 10:43 AM, Mason Wells wrote: > > External Email - Use Caution > > > > Great, thanks again Bruce. > > Doug, can you confirm this is the process for taking a filtered_func file and getting it onto the freesurfer surface ready for analysis? > > > > 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 > > Tel: 02920 879628 > > Web: Cardiff University webpage <https://www.cardiff.ac.uk/people/research-students/view/974214-> > > 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 > > Ffôn: 02920 879628 > > > > > > On 17/04/2020, 15:32, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Bruce Fischl" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of fis...@nmr.mgh.harvard.edu> wrote: > > > > oh, then you probably want to use bbreg to register it and mri_vol2surf > > to sample it onto the surface. Doug is the expert on this and can > > add/correct if this is not the whole story :) > > > > cheers > > Bruce > > On Fri, 17 Apr 2020, Mason > > Wells wrote: > > > > > External Email - Use Caution > > > > > > Hi Bruce, > > > > > > The only pre-processing I have done is the motion correction, high pass filtering and distortion correction. So, as far as I know it is still in the volume and in the original functional space. > > > > > > 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 > > > Tel: 02920 879628 > > > Web: Cardiff University webpage <https://www.cardiff.ac.uk/people/research-students/view/974214-> > > > 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 > > > Ffôn: 02920 879628 > > > > > > > > > On 17/04/2020, 15:11, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Bruce Fischl" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of fis...@nmr.mgh.harvard.edu> wrote: > > > > > > Hi Mason > > > > > > is your filtered_func file already sampled onto the surface or is it a > > > volume? > > > > > > cheers > > > Bruce > > > On Fri, 17 Apr 2020, Mason Wells wrote: > > > > > > > > > > > External Email - Use Caution > > > > > > > > Hi all, > > > > > > > > > > > > > > > > I am trying to use an analysis package that works on surface based data > > > > (SamSrf). I have ran Feat and have a filtered_func file which is of course > > > > the motion corrected/unwarped version of my EPI. However, I need some advice > > > > on how to get these data onto the Freesurfer surface. I have found this > > > > page, but I wanted to double check this is the most up-to-date pipeline. On > > > > the page it suggests using the same DOF as used in Feat, I use BBR so this > > > > seems a little redundant. Has anyone on these lists got any experience of > > > > getting filtered_func onto the Freesurfer surface? > > > > > > > > > > > > > > > > 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 > > > > > > > > Tel: 02920 879628 > > > > > > > > Web: Cardiff University webpage > > > > > > > > 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 > > > > > > > > Ffôn: 02920 879628 > > > > > > > > > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu > > > https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&data=02%7C01%7CWellsMT1%40cardiff.ac.uk%7Cd1f3f081039a4d49340808d7e2f660e9%7Cbdb74b3095684856bdbf06759778fcbc%7C1%7C0%7C637227420124409244&sdata=WrdlJkmV7zua1ZxLeZCbPjq9bDNUwWulOTTbnJwWXSI%3D&reserved=0 > > > > > > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&data=02%7C01%7CWellsMT1%40cardiff.ac.uk%7Cd1f3f081039a4d49340808d7e2f660e9%7Cbdb74b3095684856bdbf06759778fcbc%7C1%7C0%7C637227420124409244&sdata=WrdlJkmV7zua1ZxLeZCbPjq9bDNUwWulOTTbnJwWXSI%3D&reserved=0 > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&data=02%7C01%7CWellsMT1%40cardiff.ac.uk%7Cd1f3f081039a4d49340808d7e2f660e9%7Cbdb74b3095684856bdbf06759778fcbc%7C1%7C0%7C637227420124419237&sdata=eb1fDHszb4dmMtgLO0XBNdDD9jk0Li3XaQ4uLc1MphM%3D&reserved=0 > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&data=02%7C01%7CWellsMT1%40cardiff.ac.uk%7Cd1f3f081039a4d49340808d7e2f660e9%7Cbdb74b3095684856bdbf06759778fcbc%7C1%7C0%7C637227420124419237&sdata=eb1fDHszb4dmMtgLO0XBNdDD9jk0Li3XaQ4uLc1MphM%3D&reserved=0 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&data=02%7C01%7CWellsMT1%40cardiff.ac.uk%7Cd1f3f081039a4d49340808d7e2f660e9%7Cbdb74b3095684856bdbf06759778fcbc%7C1%7C0%7C637227420124419237&sdata=eb1fDHszb4dmMtgLO0XBNdDD9jk0Li3XaQ4uLc1MphM%3D&reserved=0 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
