Hi Mason
not sure we can help if everything looks good in freeview. Doesn't that
make it a SamSrf issue? Or an interface between the two packages? Have you
checked with their support?
cheers
Bruce
On Thu, 26 Mar 2020, Mason Wells wrote:
External Email - Use Caution
In the event that Bruce might not be able to help. I ask if anyone else on the
list has experience with the problem described in this thread? Any help would
be greatly appreciated.
Best wishes,
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, 18:38, "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,
Ok, great. I just thought some sections of white matter had not been traced
in their entirety (see red crosshair in attached image). If you think this all
looks reasonable, please can you advise on the misaligned as outlined in the
original post?
Best wishes,
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, 17:29, "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
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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