External Email - Use Caution
Hi there,
I am having a weird problem with freeview… When l load some volumes and some surfaces together, I can’t see the surfaces because they are hidden ‘behind’ the volumes. They normally sit on top, but now I can only see them if I toggle off the volumes – which is not useful as I need both at once.
They are definitely in alignment as I can see them when I toggle, and when I look at old data that I know I could view properly (and surfaces-volumes are in alignment) I have the same issue. I can't move them up, as you can only move position within volumes and surfaces. I tried to attach a video but my email got bounced for being too large - happy to send directly if it is helpful
I am using the below code to load things (though have also manually loaded stuff in freeview). The code has not changed since it worked in the past…
I have tried searching the freesurfer help, but can’t find anything on my issue… Any help would be appreciated
Thanks!
Harriet
p.s., I am using freesurfer/ freeview on a remote machine of my university. They inform me no updates have been performed
CODE
freeview -v mri/T1.mgz \
mri/brainmask.mgz \
mri/wm.mgz:visible=0 \
-f surf/lh.smoothwm:edgecolor=yellow \
surf/lh.pial:edgecolor=red \
-viewport cor -layout 1
It sounds like a remote display issue. Are you connecting from a Windows machine? If so what x-term software do you use?
Ruopeng
On Feb 17, 2022, at 5:15 PM, Harriet Dempsey-Jones <h.dempseyjones@uq.edu.aumailto:h.dempseyjones@uq.edu.au> wrote:
External Email - Use Caution
Hi there,
I am having a weird problem with freeview… When l load some volumes and some surfaces together, I can’t see the surfaces because they are hidden ‘behind’ the volumes. They normally sit on top, but now I can only see them if I toggle off the volumes – which is not useful as I need both at once.
They are definitely in alignment as I can see them when I toggle, and when I look at old data that I know I could view properly (and surfaces-volumes are in alignment) I have the same issue. I can't move them up, as you can only move position within volumes and surfaces. I tried to attach a video but my email got bounced for being too large - happy to send directly if it is helpful
I am using the below code to load things (though have also manually loaded stuff in freeview). The code has not changed since it worked in the past…
I have tried searching the freesurfer help, but can’t find anything on my issue… Any help would be appreciated
Thanks!
Harriet
p.s., I am using freesurfer/ freeview on a remote machine of my university. They inform me no updates have been performed
CODE
freeview -v mri/T1.mgz \ mri/brainmask.mgz \ mri/wm.mgz:visible=0 \ -f surf/lh.smoothwm:edgecolor=yellow \ surf/lh.pial:edgecolor=red \ -viewport cor -layout 1
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Hi there,
Thank you for your response!
I'm not sure 100% what the answer to this is - I am connecting to the remote machine from a mac (well, two different macs, my home and work macs).
I am not sure what the x-term software is. Do you mean the terminal I use inside the remote desktop to open freeview? (see image below)
Thank you,
Harriet
[cid:94e53025-671d-44fb-916a-1586a218dd14]
Dr Harriet Dempsey-Jones
Postdoctoral Researcher
School of Psychology
The University of Queensland
Brisbane Qld 4072 Australia
E h.dempseyjones@uq.edu.aumailto:h.dempseyjones@uq.edu.au W uq.edu.auhttp://secure-web.cisco.com/1g0mnyf7Mh5mlYyGV5FOnPmMxbqxAL20rRleOF-_ytgqGNG3HgzFcSZM9S-PhyvJTsDcJtkbt5UCtI1slB22dhxaoHwz6EcU_nqwJUpL9NK3ekqPIeRKJPflpVl7JSpafLxkz0HmbVpqja_n-wwaz1-WEz0qMP3WQhszo1AsJBCwj1uCcROh3VljV_jePxtEOQXO9QtPhFnUx2h1QaQAqReC1ZcstRtYySPVFL9HTgKoLutYRwl4gDrH2xk6ZIMLcseFhoI5IsUt8vnaxsIkWJZyLFFzvvgYfASQFEZuHR1nFMbQAMyQ8tmZX0zWApafsLcfGxuo7xe421XP5W7YzmA/http%3A%2F%2Fwww.uq.edu.au%2F
[cid:dd420d9d-9395-40fa-b225-3362183cfdc8]
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Wang, Ruopeng RWANG4@MGH.HARVARD.EDU Sent: Friday, 18 February 2022 8:25 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Freeview problem - can't see surfaces, hidden behind volumes
It sounds like a remote display issue. Are you connecting from a Windows machine? If so what x-term software do you use?
Ruopeng
On Feb 17, 2022, at 5:15 PM, Harriet Dempsey-Jones <h.dempseyjones@uq.edu.aumailto:h.dempseyjones@uq.edu.au> wrote:
External Email - Use Caution
Hi there,
I am having a weird problem with freeview… When l load some volumes and some surfaces together, I can’t see the surfaces because they are hidden ‘behind’ the volumes. They normally sit on top, but now I can only see them if I toggle off the volumes – which is not useful as I need both at once.
They are definitely in alignment as I can see them when I toggle, and when I look at old data that I know I could view properly (and surfaces-volumes are in alignment) I have the same issue. I can't move them up, as you can only move position within volumes and surfaces. I tried to attach a video but my email got bounced for being too large - happy to send directly if it is helpful
I am using the below code to load things (though have also manually loaded stuff in freeview). The code has not changed since it worked in the past…
I have tried searching the freesurfer help, but can’t find anything on my issue… Any help would be appreciated
Thanks!
Harriet
p.s., I am using freesurfer/ freeview on a remote machine of my university. They inform me no updates have been performed
CODE
freeview -v mri/T1.mgz \ mri/brainmask.mgz \ mri/wm.mgz:visible=0 \ -f surf/lh.smoothwm:edgecolor=yellow \ surf/lh.pial:edgecolor=red \ -viewport cor -layout 1
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1V_UMb9QcgGObRM53sU8GZmXY-nAeO6X4ms1XnA53o62Eaz...
That question was for Windows. How do you connect to the remote machine from your mac? via VNC? Nomachine?
On Feb 18, 2022, at 1:02 AM, Harriet Dempsey-Jones <h.dempseyjones@uq.edu.aumailto:h.dempseyjones@uq.edu.au> wrote:
External Email - Use Caution
Hi there,
Thank you for your response!
I'm not sure 100% what the answer to this is - I am connecting to the remote machine from a mac (well, two different macs, my home and work macs).
I am not sure what the x-term software is. Do you mean the terminal I use inside the remote desktop to open freeview? (see image below)
Thank you,
Harriet
<image.png>
Dr Harriet Dempsey-Jones Postdoctoral Researcher
School of Psychology The University of Queensland Brisbane Qld 4072 Australia
E h.dempseyjones@uq.edu.aumailto:h.dempseyjones@uq.edu.au W uq.edu.auhttp://secure-web.cisco.com/1g0mnyf7Mh5mlYyGV5FOnPmMxbqxAL20rRleOF-_ytgqGNG3HgzFcSZM9S-PhyvJTsDcJtkbt5UCtI1slB22dhxaoHwz6EcU_nqwJUpL9NK3ekqPIeRKJPflpVl7JSpafLxkz0HmbVpqja_n-wwaz1-WEz0qMP3WQhszo1AsJBCwj1uCcROh3VljV_jePxtEOQXO9QtPhFnUx2h1QaQAqReC1ZcstRtYySPVFL9HTgKoLutYRwl4gDrH2xk6ZIMLcseFhoI5IsUt8vnaxsIkWJZyLFFzvvgYfASQFEZuHR1nFMbQAMyQ8tmZX0zWApafsLcfGxuo7xe421XP5W7YzmA/http%3A%2F%2Fwww.uq.edu.au%2F
<Outlook-yoeliosc.jpg>
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Wang, Ruopeng <RWANG4@MGH.HARVARD.EDUmailto:RWANG4@MGH.HARVARD.EDU> Sent: Friday, 18 February 2022 8:25 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Freeview problem - can't see surfaces, hidden behind volumes
It sounds like a remote display issue. Are you connecting from a Windows machine? If so what x-term software do you use?
Ruopeng
On Feb 17, 2022, at 5:15 PM, Harriet Dempsey-Jones <h.dempseyjones@uq.edu.aumailto:h.dempseyjones@uq.edu.au> wrote:
External Email - Use Caution
Hi there,
I am having a weird problem with freeview… When l load some volumes and some surfaces together, I can’t see the surfaces because they are hidden ‘behind’ the volumes. They normally sit on top, but now I can only see them if I toggle off the volumes – which is not useful as I need both at once.
They are definitely in alignment as I can see them when I toggle, and when I look at old data that I know I could view properly (and surfaces-volumes are in alignment) I have the same issue. I can't move them up, as you can only move position within volumes and surfaces. I tried to attach a video but my email got bounced for being too large - happy to send directly if it is helpful
I am using the below code to load things (though have also manually loaded stuff in freeview). The code has not changed since it worked in the past…
I have tried searching the freesurfer help, but can’t find anything on my issue… Any help would be appreciated
Thanks!
Harriet
p.s., I am using freesurfer/ freeview on a remote machine of my university. They inform me no updates have been performed
CODE
freeview -v mri/T1.mgz \ mri/brainmask.mgz \ mri/wm.mgz:visible=0 \ -f surf/lh.smoothwm:edgecolor=yellow \ surf/lh.pial:edgecolor=red \ -viewport cor -layout 1
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://secure-web.cisco.com/1V_UMb9QcgGObRM53sU8GZmXY-nAeO6X4ms1XnA53o62Eaz7TKRHVcP5Y53B7E8grLT6Hh51rlDua5xCSIMqbNEV8z4P2TPWJxVbaG_rv1bCKuD53qasF6dof5OZ1n-RSszDqy2-_psIqmLFxPRvfGMsHMRWbJQNxhszALDq6HcDarhzgqnSbaeDq-wFrBHpPeVLRk2QxPQ2BcgdOL_QXFjYJtbRNxLquIlLo4sgPd0SK0z73ROXVVua9KgbQDSA-iEyNTsvDPrtafFi5XH3VUZhnjcKNMpboBWbu34QmmFoBI6FanKONugb2DpcTZzxsSnmyYpsRYcK7DVXyvPLi4w/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Hi Ruopeng,
My apologies – I am not completely across all the details of my remote machine access and a bit unfamiliar with the terminology.
I have attached below details of how I connect to the remote windows machine from my mac. I first open a VPN and enter my university details, I then hit this page where I enter my university details again and it takes me through.
Looks like it is powered by FastX from StarNet, I think? Is this the detail you meant?
Thank you again for your help,
Harriet
[cid:image001.png@01D82719.1C7B7BF0]
The above is an image so I included the links here:
FastX link: https://secure-web.cisco.com/1l6q0I7n4VYN05ZCq7ruEwTR97Gp6VXIhUH27rZA5UpL9zi...
Build 3.2.34 link: https://secure-web.cisco.com/1Kl5EpdIPbDRC6a61pkfp7FHRJPpw6OTCKXOKr0fy4Czohu...
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Wang, Ruopeng RWANG4@MGH.HARVARD.EDU Date: Saturday, 19 February 2022 at 1:28 am To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Freeview problem - can't see surfaces, hidden behind volumes That question was for Windows. How do you connect to the remote machine from your mac? via VNC? Nomachine?
On Feb 18, 2022, at 1:02 AM, Harriet Dempsey-Jones <h.dempseyjones@uq.edu.aumailto:h.dempseyjones@uq.edu.au> wrote:
External Email - Use Caution Hi there,
Thank you for your response!
I'm not sure 100% what the answer to this is - I am connecting to the remote machine from a mac (well, two different macs, my home and work macs).
I am not sure what the x-term software is. Do you mean the terminal I use inside the remote desktop to open freeview? (see image below)
Thank you,
Harriet
<image.png>
Dr Harriet Dempsey-Jones Postdoctoral Researcher School of Psychology The University of Queensland Brisbane Qld 4072 Australia
E h.dempseyjones@uq.edu.aumailto:h.dempseyjones@uq.edu.au W uq.edu.auhttp://secure-web.cisco.com/1g0mnyf7Mh5mlYyGV5FOnPmMxbqxAL20rRleOF-_ytgqGNG3HgzFcSZM9S-PhyvJTsDcJtkbt5UCtI1slB22dhxaoHwz6EcU_nqwJUpL9NK3ekqPIeRKJPflpVl7JSpafLxkz0HmbVpqja_n-wwaz1-WEz0qMP3WQhszo1AsJBCwj1uCcROh3VljV_jePxtEOQXO9QtPhFnUx2h1QaQAqReC1ZcstRtYySPVFL9HTgKoLutYRwl4gDrH2xk6ZIMLcseFhoI5IsUt8vnaxsIkWJZyLFFzvvgYfASQFEZuHR1nFMbQAMyQ8tmZX0zWApafsLcfGxuo7xe421XP5W7YzmA/http%3A%2F%2Fwww.uq.edu.au%2F
<Outlook-yoeliosc.jpg>
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Wang, Ruopeng <RWANG4@MGH.HARVARD.EDUmailto:RWANG4@MGH.HARVARD.EDU> Sent: Friday, 18 February 2022 8:25 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Freeview problem - can't see surfaces, hidden behind volumes
It sounds like a remote display issue. Are you connecting from a Windows machine? If so what x-term software do you use?
Ruopeng
On Feb 17, 2022, at 5:15 PM, Harriet Dempsey-Jones <h.dempseyjones@uq.edu.aumailto:h.dempseyjones@uq.edu.au> wrote:
External Email - Use Caution Hi there,
I am having a weird problem with freeview… When l load some volumes and some surfaces together, I can’t see the surfaces because they are hidden ‘behind’ the volumes. They normally sit on top, but now I can only see them if I toggle off the volumes – which is not useful as I need both at once.
They are definitely in alignment as I can see them when I toggle, and when I look at old data that I know I could view properly (and surfaces-volumes are in alignment) I have the same issue. I can't move them up, as you can only move position within volumes and surfaces. I tried to attach a video but my email got bounced for being too large - happy to send directly if it is helpful
I am using the below code to load things (though have also manually loaded stuff in freeview). The code has not changed since it worked in the past…
I have tried searching the freesurfer help, but can’t find anything on my issue… Any help would be appreciated
Thanks!
Harriet
p.s., I am using freesurfer/ freeview on a remote machine of my university. They inform me no updates have been performed
CODE
freeview -v mri/T1.mgz \ mri/brainmask.mgz \ mri/wm.mgz:visible=0 \ -f surf/lh.smoothwm:edgecolor=yellow \ surf/lh.pial:edgecolor=red \ -viewport cor -layout 1
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1XBg-I1lC4i9MtQjrhF1DXiEP_h9NLiP6BzsFEGQLWpZlar...https://secure-web.cisco.com/1V_UMb9QcgGObRM53sU8GZmXY-nAeO6X4ms1XnA53o62Eaz7TKRHVcP5Y53B7E8grLT6Hh51rlDua5xCSIMqbNEV8z4P2TPWJxVbaG_rv1bCKuD53qasF6dof5OZ1n-RSszDqy2-_psIqmLFxPRvfGMsHMRWbJQNxhszALDq6HcDarhzgqnSbaeDq-wFrBHpPeVLRk2QxPQ2BcgdOL_QXFjYJtbRNxLquIlLo4sgPd0SK0z73ROXVVua9KgbQDSA-iEyNTsvDPrtafFi5XH3VUZhnjcKNMpboBWbu34QmmFoBI6FanKONugb2DpcTZzxsSnmyYpsRYcK7DVXyvPLi4w/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1XBg-I1lC4i9MtQjrhF1DXiEP_h9NLiP6BzsFEGQLWpZlar...
freesurfer@nmr.mgh.harvard.edu
-
Harriet Dempsey-Jones -
Wang, Ruopeng