Re: [Freesurfer] Misalignment of boundaries and T1 (Freesurfer/SamSrf)

something like

freeview -v $SUBJECTS_DIR/<subject name>/mri/norm.mgz \ -f $SUBJECTS_DIR/<subject name>/surf/?h.white

cheers Bruce

On Wed, 25 Mar 2020, Mason Wells wrote:

   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

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