External Email - Use Caution
Hi Bruce,
Thanks for getting back to me. Sorry, but I am not sure I follow what you mean here. Could you please explain how I would check this?
Thanks again for 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: 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 25/03/2020, 16:11, "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
can you confirm that things look ok within FreeSurfer if you look at the surface over the volume in freeview?
cheers Bruce On Wed, 25 Mar 2020, Mason Wells wrote:
> > External Email - Use Caution > > Hello Freesurfer developers, > > > > I am using Freesurfer and SamSrf for prf mapping. I have ran the recon-all > command which finished without errors. However, the white/grey matter > boundaries are significantly misaligned with the subjects T1 (images > attached). Below are the steps I have taken to reach this point in the > analysis: > > > > 1. Run fsl_anat to get a bias corrected T1 and T1_biascor_brain. > 2. Ran Feat > > · Distortion correction of the EPI > > · Motion correction > > · No smoothing > > · Highpass filter > > · No registration to whole brain > > · Register to T1_biascorr_brain > > · Register to standard space > > 3. Ran recon-all on T1_biascorr > 4. Convert T1/T1_brain/orig(001) from mgz to nii > 5. Check registration (using the SurfaceProjection command from the SamSrf > package) which leads to the attached images named S1 and S1. > > > > Freesurfer version: > freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c > > Platform: Linux 5.3.0-40-generic x86_64 > > Uname: Linux masontwells-VIG800S 5.3.0-40-generic #32~18.04.1-Ubuntu SMP Mon > Feb 3 14:05:59 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux > > > > As you can see, the registration is significantly misaligned. > > Can anyone offer any advice on this/suggest a way to rectify it? > > > > > > 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 > > > > >