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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
1. Ran recon-all on T1_biascorr 2. Convert T1/T1_brain/orig(001) from mgz to nii 3. 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.ukmailto:WellsMT1@cardiff.ac.uk Tel: 02920 879628 Web: Cardiff University webpagehttps://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.ukmailto:WellsMT1@caerdydd.ac.uk Ffôn: 02920 879628
