External Email - Use Caution
Dear Freesurfers,
we have installed the updated Freeview version in the development version of Freesurfer (Centos 6, 18 january build), but Bert images appear displaced when they are loaded with this version of Freeview. The same displacement occurs when other dataset is used. Please find attached a screenshot to display the issue. Would you please help me to solve the problem?
Thank you in advance.
Best, Jose
Can you share the freeview command you run to load the these data?
Ruopeng
On Jan 31, 2019, at 7:31 AM, Laboratorio de Neurociencia Funcional neuroaginglnf@gmail.com wrote:
External Email - Use CautionDear Freesurfers,
we have installed the updated Freeview version in the development version of Freesurfer (Centos 6, 18 january build), but Bert images appear displaced when they are loaded with this version of Freeview. The same displacement occurs when other dataset is used. Please find attached a screenshot to display the issue. Would you please help me to solve the problem?
Thank you in advance.
Best, Jose <Image displacement_Freeview.png>_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Sure, commands are copied below:
*File > Run Command*
*-v /usr/local/freesurfer/subjects/OSM_0/mri/T1.mgz*
*-v /usr/local/freesurfer/subjects/OSM_0/mri/brainmask.mgz*
*-**f /usr/local/freesurfer/subjects/OSM_0/surf/lh.white:edgecolor=yellow*
*-f /usr/local/freesurfer/subjects/OSM_0/surf/lh.pial:edgecolor=red*
*-f /usr/local/freesurfer/subjects/OSM_0/surf/rh.white:edgecolor=yellow*
*-f /usr/local/freesurfer/subjects/OSM_0/surf/rh.pial:edgecolor=red*
Looking forward your comments.
Best, Jose
El jue., 31 ene. 2019 a las 14:39, Ruopeng Wang (rpwang@nmr.mgh.harvard.edu) escribió:
Can you share the freeview command you run to load the these data?
Ruopeng
On Jan 31, 2019, at 7:31 AM, Laboratorio de Neurociencia Funcional < neuroaginglnf@gmail.com> wrote:
External Email - Use CautionDear Freesurfers,
we have installed the updated Freeview version in the development version of Freesurfer (Centos 6, 18 january build), but Bert images appear displaced when they are loaded with this version of Freeview. The same displacement occurs when other dataset is used. Please find attached a screenshot to display the issue. Would you please help me to solve the problem?
Thank you in advance.
Best, Jose
<Image displacement_Freeview.png> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Your screenshot appears to be from burt data but I assume it was loaded with similar commands. I could not replicate the displacement with burt data. Would it be possible to send me T1.mgz and lh.white file from this OSM_0 subject?
Thanks, Ruopeng
On Jan 31, 2019, at 9:18 AM, Laboratorio de Neurociencia Funcional neuroaginglnf@gmail.com wrote:
External Email - Use CautionSure, commands are copied below: File > Run Command
-v /usr/local/freesurfer/subjects/OSM_0/mri/T1.mgz
-v /usr/local/freesurfer/subjects/OSM_0/mri/brainmask.mgz
-f /usr/local/freesurfer/subjects/OSM_0/surf/lh.white:edgecolor=yellow
-f /usr/local/freesurfer/subjects/OSM_0/surf/lh.pial:edgecolor=red
-f /usr/local/freesurfer/subjects/OSM_0/surf/rh.white:edgecolor=yellow
-f /usr/local/freesurfer/subjects/OSM_0/surf/rh.pial:edgecolor=red
Looking forward your comments.
Best, Jose
El jue., 31 ene. 2019 a las 14:39, Ruopeng Wang (<rpwang@nmr.mgh.harvard.edu mailto:rpwang@nmr.mgh.harvard.edu>) escribió: Can you share the freeview command you run to load the these data?
Ruopeng
On Jan 31, 2019, at 7:31 AM, Laboratorio de Neurociencia Funcional <neuroaginglnf@gmail.com mailto:neuroaginglnf@gmail.com> wrote:
External Email - Use CautionDear Freesurfers,
we have installed the updated Freeview version in the development version of Freesurfer (Centos 6, 18 january build), but Bert images appear displaced when they are loaded with this version of Freeview. The same displacement occurs when other dataset is used. Please find attached a screenshot to display the issue. Would you please help me to solve the problem?
Thank you in advance.
Best, Jose <Image displacement_Freeview.png>_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Hi Ruopeng,
we have tried these commands with Bert and with different datasets and the problem persists. Could the problem be related to the way that we have installed Freeview or something wrong between Freeview and the Ubuntu version that we are using (16.04 TLS)?
Best, Jose
El jue., 31 ene. 2019 a las 15:32, Ruopeng Wang (rpwang@nmr.mgh.harvard.edu) escribió:
Your screenshot appears to be from burt data but I assume it was loaded with similar commands. I could not replicate the displacement with burt data. Would it be possible to send me T1.mgz and lh.white file from this OSM_0 subject?
Thanks, Ruopeng
On Jan 31, 2019, at 9:18 AM, Laboratorio de Neurociencia Funcional < neuroaginglnf@gmail.com> wrote:
External Email - Use CautionSure, commands are copied below:
*File > Run Command*
*-v /usr/local/freesurfer/subjects/OSM_0/mri/T1.mgz*
*-v /usr/local/freesurfer/subjects/OSM_0/mri/brainmask.mgz*
*-**f /usr/local/freesurfer/subjects/OSM_0/surf/lh.white:edgecolor=yellow*
*-f /usr/local/freesurfer/subjects/OSM_0/surf/lh.pial:edgecolor=red*
*-f /usr/local/freesurfer/subjects/OSM_0/surf/rh.white:edgecolor=yellow*
*-f /usr/local/freesurfer/subjects/OSM_0/surf/rh.pial:edgecolor=red*
Looking forward your comments.
Best, Jose
El jue., 31 ene. 2019 a las 14:39, Ruopeng Wang (< rpwang@nmr.mgh.harvard.edu>) escribió:
Can you share the freeview command you run to load the these data?
Ruopeng
On Jan 31, 2019, at 7:31 AM, Laboratorio de Neurociencia Funcional < neuroaginglnf@gmail.com> wrote:
External Email - Use CautionDear Freesurfers,
we have installed the updated Freeview version in the development version of Freesurfer (Centos 6, 18 january build), but Bert images appear displaced when they are loaded with this version of Freeview. The same displacement occurs when other dataset is used. Please find attached a screenshot to display the issue. Would you please help me to solve the problem?
Thank you in advance.
Best, Jose
<Image displacement_Freeview.png> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
That’s unlikely. Did FS 6.0 have the same problem?
On Jan 31, 2019, at 9:59 AM, Laboratorio de Neurociencia Funcional neuroaginglnf@gmail.com wrote:
External Email - Use CautionHi Ruopeng,
we have tried these commands with Bert and with different datasets and the problem persists. Could the problem be related to the way that we have installed Freeview or something wrong between Freeview and the Ubuntu version that we are using (16.04 TLS)?
Best, Jose
El jue., 31 ene. 2019 a las 15:32, Ruopeng Wang (<rpwang@nmr.mgh.harvard.edu mailto:rpwang@nmr.mgh.harvard.edu>) escribió: Your screenshot appears to be from burt data but I assume it was loaded with similar commands. I could not replicate the displacement with burt data. Would it be possible to send me T1.mgz and lh.white file from this OSM_0 subject?
Thanks, Ruopeng
On Jan 31, 2019, at 9:18 AM, Laboratorio de Neurociencia Funcional <neuroaginglnf@gmail.com mailto:neuroaginglnf@gmail.com> wrote:
External Email - Use CautionSure, commands are copied below: File > Run Command
-v /usr/local/freesurfer/subjects/OSM_0/mri/T1.mgz
-v /usr/local/freesurfer/subjects/OSM_0/mri/brainmask.mgz
-f /usr/local/freesurfer/subjects/OSM_0/surf/lh.white:edgecolor=yellow
-f /usr/local/freesurfer/subjects/OSM_0/surf/lh.pial:edgecolor=red
-f /usr/local/freesurfer/subjects/OSM_0/surf/rh.white:edgecolor=yellow
-f /usr/local/freesurfer/subjects/OSM_0/surf/rh.pial:edgecolor=red
Looking forward your comments.
Best, Jose
El jue., 31 ene. 2019 a las 14:39, Ruopeng Wang (<rpwang@nmr.mgh.harvard.edu mailto:rpwang@nmr.mgh.harvard.edu>) escribió: Can you share the freeview command you run to load the these data?
Ruopeng
On Jan 31, 2019, at 7:31 AM, Laboratorio de Neurociencia Funcional <neuroaginglnf@gmail.com mailto:neuroaginglnf@gmail.com> wrote:
External Email - Use CautionDear Freesurfers,
we have installed the updated Freeview version in the development version of Freesurfer (Centos 6, 18 january build), but Bert images appear displaced when they are loaded with this version of Freeview. The same displacement occurs when other dataset is used. Please find attached a screenshot to display the issue. Would you please help me to solve the problem?
Thank you in advance.
Best, Jose <Image displacement_Freeview.png>_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
No, we didn't have the same problem neither with Freesurfer 6.0 or with the development Freesurfer version. The problem only arises when we display FS images with Freeview using Freesurfer (6.0 or development version). For that reason, I asked you about issues installing Freeview, or wrong interaction between Ubuntu and Freeview. Any suggestion?
El jue., 31 ene. 2019 a las 16:30, Ruopeng Wang (rpwang@nmr.mgh.harvard.edu) escribió:
That’s unlikely. Did FS 6.0 have the same problem?
On Jan 31, 2019, at 9:59 AM, Laboratorio de Neurociencia Funcional < neuroaginglnf@gmail.com> wrote:
External Email - Use CautionHi Ruopeng,
we have tried these commands with Bert and with different datasets and the problem persists. Could the problem be related to the way that we have installed Freeview or something wrong between Freeview and the Ubuntu version that we are using (16.04 TLS)?
Best, Jose
El jue., 31 ene. 2019 a las 15:32, Ruopeng Wang (< rpwang@nmr.mgh.harvard.edu>) escribió:
Your screenshot appears to be from burt data but I assume it was loaded with similar commands. I could not replicate the displacement with burt data. Would it be possible to send me T1.mgz and lh.white file from this OSM_0 subject?
Thanks, Ruopeng
On Jan 31, 2019, at 9:18 AM, Laboratorio de Neurociencia Funcional < neuroaginglnf@gmail.com> wrote:
External Email - Use CautionSure, commands are copied below:
*File > Run Command*
*-v /usr/local/freesurfer/subjects/OSM_0/mri/T1.mgz*
*-v /usr/local/freesurfer/subjects/OSM_0/mri/brainmask.mgz*
*-**f /usr/local/freesurfer/subjects/OSM_0/surf/lh.white:edgecolor=yellow*
*-f /usr/local/freesurfer/subjects/OSM_0/surf/lh.pial:edgecolor=red*
*-f /usr/local/freesurfer/subjects/OSM_0/surf/rh.white:edgecolor=yellow*
*-f /usr/local/freesurfer/subjects/OSM_0/surf/rh.pial:edgecolor=red*
Looking forward your comments.
Best, Jose
El jue., 31 ene. 2019 a las 14:39, Ruopeng Wang (< rpwang@nmr.mgh.harvard.edu>) escribió:
Can you share the freeview command you run to load the these data?
Ruopeng
On Jan 31, 2019, at 7:31 AM, Laboratorio de Neurociencia Funcional < neuroaginglnf@gmail.com> wrote:
External Email - Use CautionDear Freesurfers,
we have installed the updated Freeview version in the development version of Freesurfer (Centos 6, 18 january build), but Bert images appear displaced when they are loaded with this version of Freeview. The same displacement occurs when other dataset is used. Please find attached a screenshot to display the issue. Would you please help me to solve the problem?
Thank you in advance.
Best, Jose
<Image displacement_Freeview.png> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Can you send us a T1.mgz file along with a lh.white file that do not align when loaded in freeview?
On 1/31/19 10:47 AM, Laboratorio de Neurociencia Funcional wrote:
No, we didn't have the same problem neither with Freesurfer 6.0 or with the development Freesurfer version. The problem only arises when we display FS images with Freeview using Freesurfer (6.0 or development version). For that reason, I asked you about issues installing Freeview, or wrong interaction between Ubuntu and Freeview. Any suggestion?
El jue., 31 ene. 2019 a las 16:30, Ruopeng Wang (<rpwang@nmr.mgh.harvard.edu mailto:rpwang@nmr.mgh.harvard.edu>) escribió:
That’s unlikely. Did FS 6.0 have the same problem?On Jan 31, 2019, at 9:59 AM, Laboratorio de Neurociencia Funcional <neuroaginglnf@gmail.com <mailto:neuroaginglnf@gmail.com>> wrote: External Email - Use Caution Hi Ruopeng, we have tried these commands with Bert and with different datasets and the problem persists. Could the problem be related to the way that we have installed Freeview or something wrong between Freeview and the Ubuntu version that we are using (16.04 TLS)? Best, Jose El jue., 31 ene. 2019 a las 15:32, Ruopeng Wang (<rpwang@nmr.mgh.harvard.edu <mailto:rpwang@nmr.mgh.harvard.edu>>) escribió: Your screenshot appears to be from burt data but I assume it was loaded with similar commands. I could not replicate the displacement with burt data. Would it be possible to send me T1.mgz and lh.white file from this OSM_0 subject? Thanks, RuopengOn Jan 31, 2019, at 9:18 AM, Laboratorio de Neurociencia Funcional <neuroaginglnf@gmail.com <mailto:neuroaginglnf@gmail.com>> wrote: External Email - Use Caution Sure, commands are copied below: *File > Run Command* *-v /usr/local/freesurfer/subjects/OSM_0/mri/T1.mgz* *-v /usr/local/freesurfer/subjects/OSM_0/mri/brainmask.mgz* *-**f /usr/local/freesurfer/subjects/OSM_0/surf/lh.white:edgecolor=yellow* *-f /usr/local/freesurfer/subjects/OSM_0/surf/lh.pial:edgecolor=red* *-f /usr/local/freesurfer/subjects/OSM_0/surf/rh.white:edgecolor=yellow* *-f /usr/local/freesurfer/subjects/OSM_0/surf/rh.pial:edgecolor=red* Looking forward your comments. Best, Jose* * El jue., 31 ene. 2019 a las 14:39, Ruopeng Wang (<rpwang@nmr.mgh.harvard.edu <mailto:rpwang@nmr.mgh.harvard.edu>>) escribió: Can you share the freeview command you run to load the these data? RuopengOn Jan 31, 2019, at 7:31 AM, Laboratorio de Neurociencia Funcional <neuroaginglnf@gmail.com <mailto:neuroaginglnf@gmail.com>> wrote: External Email - Use Caution Dear Freesurfers, we have installed the updated Freeview version in the development version of Freesurfer (Centos 6, 18 january build), but Bert images appear displaced when they are loaded with this version of Freeview. The same displacement occurs when other dataset is used. Please find attached a screenshot to display the issue. Would you please help me to solve the problem? Thank you in advance. Best, Jose <Image displacement_Freeview.png>_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Please let me know how to send you these files.
El jue., 31 ene. 2019 a las 17:19, Ruopeng Wang (rpwang@nmr.mgh.harvard.edu) escribió:
Can you send us a T1.mgz file along with a lh.white file that do not align when loaded in freeview? On 1/31/19 10:47 AM, Laboratorio de Neurociencia Funcional wrote:
No, we didn't have the same problem neither with Freesurfer 6.0 or with the development Freesurfer version. The problem only arises when we display FS images with Freeview using Freesurfer (6.0 or development version). For that reason, I asked you about issues installing Freeview, or wrong interaction between Ubuntu and Freeview. Any suggestion?
El jue., 31 ene. 2019 a las 16:30, Ruopeng Wang (< rpwang@nmr.mgh.harvard.edu>) escribió:
That’s unlikely. Did FS 6.0 have the same problem?
On Jan 31, 2019, at 9:59 AM, Laboratorio de Neurociencia Funcional < neuroaginglnf@gmail.com> wrote:
External Email - Use CautionHi Ruopeng,
we have tried these commands with Bert and with different datasets and the problem persists. Could the problem be related to the way that we have installed Freeview or something wrong between Freeview and the Ubuntu version that we are using (16.04 TLS)?
Best, Jose
El jue., 31 ene. 2019 a las 15:32, Ruopeng Wang (< rpwang@nmr.mgh.harvard.edu>) escribió:
Your screenshot appears to be from burt data but I assume it was loaded with similar commands. I could not replicate the displacement with burt data. Would it be possible to send me T1.mgz and lh.white file from this OSM_0 subject?
Thanks, Ruopeng
On Jan 31, 2019, at 9:18 AM, Laboratorio de Neurociencia Funcional < neuroaginglnf@gmail.com> wrote:
External Email - Use CautionSure, commands are copied below:
*File > Run Command*
*-v /usr/local/freesurfer/subjects/OSM_0/mri/T1.mgz*
*-v /usr/local/freesurfer/subjects/OSM_0/mri/brainmask.mgz*
*-**f /usr/local/freesurfer/subjects/OSM_0/surf/lh.white:edgecolor=yellow*
*-f /usr/local/freesurfer/subjects/OSM_0/surf/lh.pial:edgecolor=red*
*-f /usr/local/freesurfer/subjects/OSM_0/surf/rh.white:edgecolor=yellow*
*-f /usr/local/freesurfer/subjects/OSM_0/surf/rh.pial:edgecolor=red*
Looking forward your comments.
Best, Jose
El jue., 31 ene. 2019 a las 14:39, Ruopeng Wang (< rpwang@nmr.mgh.harvard.edu>) escribió:
Can you share the freeview command you run to load the these data?
Ruopeng
On Jan 31, 2019, at 7:31 AM, Laboratorio de Neurociencia Funcional < neuroaginglnf@gmail.com> wrote:
External Email - Use CautionDear Freesurfers,
we have installed the updated Freeview version in the development version of Freesurfer (Centos 6, 18 january build), but Bert images appear displaced when they are loaded with this version of Freeview. The same displacement occurs when other dataset is used. Please find attached a screenshot to display the issue. Would you please help me to solve the problem?
Thank you in advance.
Best, Jose
<Image displacement_Freeview.png> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
You can send via filedrop here:
https://gate.nmr.mgh.harvard.edu/filedrop2/
Use rpwang as recipient. Thanks.
On 1/31/19 11:29 AM, Laboratorio de Neurociencia Funcional wrote:
Please let me know how to send you these files.
El jue., 31 ene. 2019 a las 17:19, Ruopeng Wang (<rpwang@nmr.mgh.harvard.edu mailto:rpwang@nmr.mgh.harvard.edu>) escribió:
Can you send us a T1.mgz file along with a lh.white file that do not align when loaded in freeview? On 1/31/19 10:47 AM, Laboratorio de Neurociencia Funcional wrote:No, we didn't have the same problem neither with Freesurfer 6.0 or with the development Freesurfer version. The problem only arises when we display FS images with Freeview using Freesurfer (6.0 or development version). For that reason, I asked you about issues installing Freeview, or wrong interaction between Ubuntu and Freeview. Any suggestion? El jue., 31 ene. 2019 a las 16:30, Ruopeng Wang (<rpwang@nmr.mgh.harvard.edu <mailto:rpwang@nmr.mgh.harvard.edu>>) escribió: That’s unlikely. Did FS 6.0 have the same problem?On Jan 31, 2019, at 9:59 AM, Laboratorio de Neurociencia Funcional <neuroaginglnf@gmail.com <mailto:neuroaginglnf@gmail.com>> wrote: External Email - Use Caution Hi Ruopeng, we have tried these commands with Bert and with different datasets and the problem persists. Could the problem be related to the way that we have installed Freeview or something wrong between Freeview and the Ubuntu version that we are using (16.04 TLS)? Best, Jose El jue., 31 ene. 2019 a las 15:32, Ruopeng Wang (<rpwang@nmr.mgh.harvard.edu <mailto:rpwang@nmr.mgh.harvard.edu>>) escribió: Your screenshot appears to be from burt data but I assume it was loaded with similar commands. I could not replicate the displacement with burt data. Would it be possible to send me T1.mgz and lh.white file from this OSM_0 subject? Thanks, RuopengOn Jan 31, 2019, at 9:18 AM, Laboratorio de Neurociencia Funcional <neuroaginglnf@gmail.com <mailto:neuroaginglnf@gmail.com>> wrote: External Email - Use Caution Sure, commands are copied below: *File > Run Command* *-v /usr/local/freesurfer/subjects/OSM_0/mri/T1.mgz* *-v /usr/local/freesurfer/subjects/OSM_0/mri/brainmask.mgz* *-**f /usr/local/freesurfer/subjects/OSM_0/surf/lh.white:edgecolor=yellow* *-f /usr/local/freesurfer/subjects/OSM_0/surf/lh.pial:edgecolor=red* *-f /usr/local/freesurfer/subjects/OSM_0/surf/rh.white:edgecolor=yellow* *-f /usr/local/freesurfer/subjects/OSM_0/surf/rh.pial:edgecolor=red* Looking forward your comments. Best, Jose* * El jue., 31 ene. 2019 a las 14:39, Ruopeng Wang (<rpwang@nmr.mgh.harvard.edu <mailto:rpwang@nmr.mgh.harvard.edu>>) escribió: Can you share the freeview command you run to load the these data? RuopengOn Jan 31, 2019, at 7:31 AM, Laboratorio de Neurociencia Funcional <neuroaginglnf@gmail.com <mailto:neuroaginglnf@gmail.com>> wrote: External Email - Use Caution Dear Freesurfers, we have installed the updated Freeview version in the development version of Freesurfer (Centos 6, 18 january build), but Bert images appear displaced when they are loaded with this version of Freeview. The same displacement occurs when other dataset is used. Please find attached a screenshot to display the issue. Would you please help me to solve the problem? Thank you in advance. Best, Jose <Image displacement_Freeview.png>_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Hi Ruopeng,
I have just uploaded the files. Thank you for your help.
Best, Jose
El jue., 31 ene. 2019 a las 17:32, Ruopeng Wang (rpwang@nmr.mgh.harvard.edu) escribió:
You can send via filedrop here:
https://gate.nmr.mgh.harvard.edu/filedrop2/
Use rpwang as recipient. Thanks. On 1/31/19 11:29 AM, Laboratorio de Neurociencia Funcional wrote:
Please let me know how to send you these files.
El jue., 31 ene. 2019 a las 17:19, Ruopeng Wang (< rpwang@nmr.mgh.harvard.edu>) escribió:
Can you send us a T1.mgz file along with a lh.white file that do not align when loaded in freeview? On 1/31/19 10:47 AM, Laboratorio de Neurociencia Funcional wrote:
No, we didn't have the same problem neither with Freesurfer 6.0 or with the development Freesurfer version. The problem only arises when we display FS images with Freeview using Freesurfer (6.0 or development version). For that reason, I asked you about issues installing Freeview, or wrong interaction between Ubuntu and Freeview. Any suggestion?
El jue., 31 ene. 2019 a las 16:30, Ruopeng Wang (< rpwang@nmr.mgh.harvard.edu>) escribió:
That’s unlikely. Did FS 6.0 have the same problem?
On Jan 31, 2019, at 9:59 AM, Laboratorio de Neurociencia Funcional < neuroaginglnf@gmail.com> wrote:
External Email - Use CautionHi Ruopeng,
we have tried these commands with Bert and with different datasets and the problem persists. Could the problem be related to the way that we have installed Freeview or something wrong between Freeview and the Ubuntu version that we are using (16.04 TLS)?
Best, Jose
El jue., 31 ene. 2019 a las 15:32, Ruopeng Wang (< rpwang@nmr.mgh.harvard.edu>) escribió:
Your screenshot appears to be from burt data but I assume it was loaded with similar commands. I could not replicate the displacement with burt data. Would it be possible to send me T1.mgz and lh.white file from this OSM_0 subject?
Thanks, Ruopeng
On Jan 31, 2019, at 9:18 AM, Laboratorio de Neurociencia Funcional < neuroaginglnf@gmail.com> wrote:
External Email - Use CautionSure, commands are copied below:
*File > Run Command*
*-v /usr/local/freesurfer/subjects/OSM_0/mri/T1.mgz*
*-v /usr/local/freesurfer/subjects/OSM_0/mri/brainmask.mgz*
*-**f /usr/local/freesurfer/subjects/OSM_0/surf/lh.white:edgecolor=yellow*
*-f /usr/local/freesurfer/subjects/OSM_0/surf/lh.pial:edgecolor=red*
*-f /usr/local/freesurfer/subjects/OSM_0/surf/rh.white:edgecolor=yellow*
*-f /usr/local/freesurfer/subjects/OSM_0/surf/rh.pial:edgecolor=red*
Looking forward your comments.
Best, Jose
El jue., 31 ene. 2019 a las 14:39, Ruopeng Wang (< rpwang@nmr.mgh.harvard.edu>) escribió:
Can you share the freeview command you run to load the these data?
Ruopeng
On Jan 31, 2019, at 7:31 AM, Laboratorio de Neurociencia Funcional < neuroaginglnf@gmail.com> wrote:
External Email - Use CautionDear Freesurfers,
we have installed the updated Freeview version in the development version of Freesurfer (Centos 6, 18 january build), but Bert images appear displaced when they are loaded with this version of Freeview. The same displacement occurs when other dataset is used. Please find attached a screenshot to display the issue. Would you please help me to solve the problem?
Thank you in advance.
Best, Jose
<Image displacement_Freeview.png> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Laboratorio de Neurociencia Funcional -
Ruopeng Wang