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: WellsMT1@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: WellsMT1@caerdydd.ac.uk Ffôn: 02920 879628
On 17/04/2020, 15:32, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of fischl@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: WellsMT1@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: WellsMT1@caerdydd.ac.uk > Ffôn: 02920 879628 > > > On 17/04/2020, 15:11, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of fischl@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: WellsMT1@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: WellsMT1@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.m... > > >