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
1. Ran recon-all on T1_biascorr 2. Convert T1/T1_brain/orig(001) from mgz to nii 3. 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.ukmailto:WellsMT1@cardiff.ac.uk Tel: 02920 879628 Web: Cardiff University webpagehttps://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.ukmailto:WellsMT1@caerdydd.ac.uk Ffôn: 02920 879628
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:
- Run fsl_anat to get a bias corrected T1 and T1_biascor_brain.
- 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
- Ran recon-all on T1_biascorr
- Convert T1/T1_brain/orig(001) from mgz to nii
- 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
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 > > > > >
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 CautionHi 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 CautionHello 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:
- Run fsl_anat to get a bias corrected T1 and T1_biascor_brain.
- 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
- Ran recon-all on T1_biascorr
- Convert T1/T1_brain/orig(001) from mgz to nii
- 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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: 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, 16:19, "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:
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 > > > > > > > > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.m... > > >
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: 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, 16:28, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Mason Wells" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of WellsMT1@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: 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, 16:19, "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:
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 > > > > > > > > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.m... > > >
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.m...
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 CautionHi 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: 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, 16:28, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Mason Wells" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of WellsMT1@cardiff.ac.uk> wrote:
External Email - Use CautionHi 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: 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, 16:19, "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:
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 > > > > > > > > > > > > > _______________________________________________ > 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%7C57fd8862f455441049d508d7d0d999a7%7Cbdb74b3095684856bdbf06759778fcbc%7C1%7C0%7C637207505312319184&sdata=RCaINVrWWVHGn4nAlzcDziyuiYDBO9HZhZ8apSzok14%3D&reserved=0 > > >
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.m...
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: 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, 17:29, "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
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: 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, 16:28, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Mason Wells" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of WellsMT1@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: 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, 16:19, "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: > > 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 > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.m... > > > > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.m... > >
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: 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, 18:38, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Mason Wells" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of WellsMT1@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: 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, 17:29, "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
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: 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, 16:28, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Mason Wells" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of WellsMT1@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: 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, 16:19, "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: > > 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 > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.m... > > > > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.m... > >
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 CautionIn 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: 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, 18:38, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Mason Wells" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of WellsMT1@cardiff.ac.uk> wrote:
External Email - Use CautionHI 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: 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, 17:29, "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 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: 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, 16:28, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Mason Wells" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of WellsMT1@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: 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, 16:19, "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: > > 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 > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > 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%7C4519acd1ab7442b9876108d7d0ebc5f4%7Cbdb74b3095684856bdbf06759778fcbc%7C1%7C0%7C637207583376235974&sdata=WaOEstHSEO9vc8uZQ0jSf4I9rFYplWeXH5mFv5tDVrM%3D&reserved=0 > > > > > > > > > _______________________________________________ > 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%7C4519acd1ab7442b9876108d7d0ebc5f4%7Cbdb74b3095684856bdbf06759778fcbc%7C1%7C0%7C637207583376235974&sdata=WaOEstHSEO9vc8uZQ0jSf4I9rFYplWeXH5mFv5tDVrM%3D&reserved=0 > >
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