Hi Mason

I can't tell from those images except that it looks reasonable
cheers
Bruce
On Wed, 25 Mar 2020, Mason Wells wrote:

External Email - Use Caution
Hi again Bruce,

I have now installed the relevant libpng packages and have freeview open. The 
segmentation doesn’t look brilliant in some areas. What do you think?

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 
<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: wells...@caerdydd.ac.uk
Ffôn: 02920 879628


On 25/03/2020, 16:28, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Mason 
Wells" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of wells...@cardiff.ac.uk> 
wrote:

           External Email - Use Caution

   Hi Bruce,

   I get the following error message when I try to load freeview

   Setting up environment for FreeSurfer/FS-FAST (and FSL)
   FREESURFER_HOME   /usr/local/freesurfer
   FSFAST_HOME       /usr/local/freesurfer/fsfast
   FSF_OUTPUT_FORMAT nii.gz
   SUBJECTS_DIR      /usr/local/freesurfer/subjects
   MNI_DIR           /usr/local/freesurfer/mni
   FSL_DIR           /usr/local/fsl
   masontwells@masontwells-VIG800S:~$ freeview
   freeview.bin: error while loading shared libraries: libpng12.so.0: cannot 
open shared object file: No such file or directory

   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 
<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: wells...@caerdydd.ac.uk
   Ffôn: 02920 879628


   On 25/03/2020, 16:19, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Bruce 
Fischl" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
fis...@nmr.mgh.harvard.edu> wrote:

       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: wells...@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: wells...@caerdydd.ac.uk
       > Ffôn: 02920 879628
       >
       >
       > On 25/03/2020, 16:11, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Bruce 
Fischl" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
fis...@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: 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
       >    >
       >    >
       >    >
       >    >
       >    >
       >
       >
       > _______________________________________________
       > Freesurfer mailing list
       > Freesurfer@nmr.mgh.harvard.edu
       > 
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