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 > https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&data=02%7C01%7CWellsMT1%40cardiff.ac.uk%7C4861d28f39774279566b08d7d0d83ebe%7Cbdb74b3095684856bdbf06759778fcbc%7C1%7C0%7C637207499492205951&sdata=NzJLQyF6%2FZP60SNwVc4DrgMHL4e7%2BgsHpGSp%2FiscGLI%3D&reserved=0 > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
