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: 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
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