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