Hi everyone,
I saw there has been posts on this before, and I know more people here at the center have this request, so I wanted to ask it again, now also for freeview: is it possible to have custom coloring on the surfaces? It is not that I need specific colors, it is just that I find the default coloring not high resolution enough to see anything more than general level differences (e.g., if I have values 0 to 100, I can only see differences between below or above 60 (red vs yellow, plus there is osme dark red for below 40), while I would like to be able to see the gradient and in between values.
Or isn't this normal behavior? Can it for example be due to using Virtual GL or due to using double precision values? I just tested using integer data (ranging from 0 to 40) and that was a bit better, but still not as good as I would expect.
Anyone any ideas on what I might be doing wrong / whether there is an alternative?
kind regards,
Frank
If you load the data as overlay in freeview, you should be able to adjust the color scale to see the gradient.
On 11/4/10 6:18 AM, f.leone@donders.ru.nl wrote:
Hi everyone,
I saw there has been posts on this before, and I know more people here at the center have this request, so I wanted to ask it again, now also for freeview: is it possible to have custom coloring on the surfaces? It is not that I need specific colors, it is just that I find the default coloring not high resolution enough to see anything more than general level differences (e.g., if I have values 0 to 100, I can only see differences between below or above 60 (red vs yellow, plus there is osme dark red for below 40), while I would like to be able to see the gradient and in between values.
Or isn't this normal behavior? Can it for example be due to using Virtual GL or due to using double precision values? I just tested using integer data (ranging from 0 to 40) and that was a bit better, but still not as good as I would expect.
Anyone any ideas on what I might be doing wrong / whether there is an alternative?
kind regards, Frank
Hi Ruopeng,
Thanks for the answer. Actually, the results I describe are already with changes to the color scale. It is still quite coarse though in my opinion.
Actually have an added wish now: I want to be able to plot circular data in freeview (retinotopic mapping), is this possible?
kind regards,
Frank
----- Oorspronkelijk bericht ----- Van: "Ruopeng Wang" rpwang@nmr.mgh.harvard.edu Aan: "Frank Leoné" f.leone@donders.ru.nl Cc: "f.leone@donders.ru.nl" f.leone@fcdonders.ru.nl, freesurfer@nmr.mgh.harvard.edu Verzonden: Donderdag 4 november 2010 15:54:14 GMT +01:00 Amsterdam / Berlijn / Bern / Rome / Stockholm / Wenen Onderwerp: Re: [Freesurfer] Custom color scale for overlays in tksurfer/freeview
If you load the data as overlay in freeview, you should be able to adjust the color scale to see the gradient.
On 11/4/10 6:18 AM, f.leone@donders.ru.nl wrote:
Hi everyone,
I saw there has been posts on this before, and I know more people here at the center have this request, so I wanted to ask it again, now also for freeview: is it possible to have custom coloring on the surfaces? It is not that I need specific colors, it is just that I find the default coloring not high resolution enough to see anything more than general level differences (e.g., if I have values 0 to 100, I can only see differences between below or above 60 (red vs yellow, plus there is osme dark red for below 40), while I would like to be able to see the gradient and in between values.
Or isn't this normal behavior? Can it for example be due to using Virtual GL or due to using double precision values? I just tested using integer data (ranging from 0 to 40) and that was a bit better, but still not as good as I would expect.
Anyone any ideas on what I might be doing wrong / whether there is an alternative?
kind regards, Frank
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
You mean even after you adjust the range of the scale, you still can only see a binary-like overlay colors? That seems to be odd.
As to visualize your circular data, you just need a customized color mapping, is that right?
On 11/4/10 11:15 AM, f.leone@donders.ru.nl wrote:
Hi Ruopeng,
Thanks for the answer. Actually, the results I describe are already with changes to the color scale. It is still quite coarse though in my opinion.
Actually have an added wish now: I want to be able to plot circular data in freeview (retinotopic mapping), is this possible?
kind regards, Frank----- Oorspronkelijk bericht ----- Van: "Ruopeng Wang"rpwang@nmr.mgh.harvard.edu Aan: "Frank Leoné"f.leone@donders.ru.nl Cc: "f.leone@donders.ru.nl"f.leone@fcdonders.ru.nl, freesurfer@nmr.mgh.harvard.edu Verzonden: Donderdag 4 november 2010 15:54:14 GMT +01:00 Amsterdam / Berlijn / Bern / Rome / Stockholm / Wenen Onderwerp: Re: [Freesurfer] Custom color scale for overlays in tksurfer/freeview
If you load the data as overlay in freeview, you should be able to adjust the color scale to see the gradient.
On 11/4/10 6:18 AM, f.leone@donders.ru.nl wrote:
Hi everyone,
I saw there has been posts on this before, and I know more people here at the center have this request, so I wanted to ask it again, now also for freeview: is it possible to have custom coloring on the surfaces? It is not that I need specific colors, it is just that I find the default coloring not high resolution enough to see anything more than general level differences (e.g., if I have values 0 to 100, I can only see differences between below or above 60 (red vs yellow, plus there is osme dark red for below 40), while I would like to be able to see the gradient and in between values.
Or isn't this normal behavior? Can it for example be due to using Virtual GL or due to using double precision values? I just tested using integer data (ranging from 0 to 40) and that was a bit better, but still not as good as I would expect.
Anyone any ideas on what I might be doing wrong / whether there is an alternative?
kind regards, FrankThe information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Yup, indeed. There are slight differences in there, but not really clear.
Yup again, a customized color mapping for overlays would fulfill all my visualization wishes, that would be great!
kind regards,
Frank
----- Original Message ----- From: "Ruopeng Wang" rpwang@nmr.mgh.harvard.edu To: "Frank Leoné" f.leone@donders.ru.nl Cc: "f.leone@donders.ru.nl" f.leone@fcdonders.ru.nl, freesurfer@nmr.mgh.harvard.edu Sent: Thursday, November 4, 2010 4:37:34 PM GMT +01:00 Amsterdam / Berlin / Bern / Rome / Stockholm / Vienna Subject: Re: [Freesurfer] Custom color scale for overlays in tksurfer/freeview
You mean even after you adjust the range of the scale, you still can only see a binary-like overlay colors? That seems to be odd.
As to visualize your circular data, you just need a customized color mapping, is that right?
On 11/4/10 11:15 AM, f.leone@donders.ru.nl wrote:
Hi Ruopeng,
Thanks for the answer. Actually, the results I describe are already with changes to the color scale. It is still quite coarse though in my opinion.
Actually have an added wish now: I want to be able to plot circular data in freeview (retinotopic mapping), is this possible?
kind regards, Frank----- Oorspronkelijk bericht ----- Van: "Ruopeng Wang"rpwang@nmr.mgh.harvard.edu Aan: "Frank Leoné"f.leone@donders.ru.nl Cc: "f.leone@donders.ru.nl"f.leone@fcdonders.ru.nl, freesurfer@nmr.mgh.harvard.edu Verzonden: Donderdag 4 november 2010 15:54:14 GMT +01:00 Amsterdam / Berlijn / Bern / Rome / Stockholm / Wenen Onderwerp: Re: [Freesurfer] Custom color scale for overlays in tksurfer/freeview
If you load the data as overlay in freeview, you should be able to adjust the color scale to see the gradient.
On 11/4/10 6:18 AM, f.leone@donders.ru.nl wrote:
Hi everyone,
I saw there has been posts on this before, and I know more people here at the center have this request, so I wanted to ask it again, now also for freeview: is it possible to have custom coloring on the surfaces? It is not that I need specific colors, it is just that I find the default coloring not high resolution enough to see anything more than general level differences (e.g., if I have values 0 to 100, I can only see differences between below or above 60 (red vs yellow, plus there is osme dark red for below 40), while I would like to be able to see the gradient and in between values.
Or isn't this normal behavior? Can it for example be due to using Virtual GL or due to using double precision values? I just tested using integer data (ranging from 0 to 40) and that was a bit better, but still not as good as I would expect.
Anyone any ideas on what I might be doing wrong / whether there is an alternative?
kind regards, FrankThe information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
OK. I'll put that on my list.
On 11/04/2010 11:56 AM, f.leone@donders.ru.nl wrote:
Yup, indeed. There are slight differences in there, but not really clear.
Yup again, a customized color mapping for overlays would fulfill all my visualization wishes, that would be great!
kind regards, Frank----- Original Message ----- From: "Ruopeng Wang"rpwang@nmr.mgh.harvard.edu To: "Frank Leoné"f.leone@donders.ru.nl Cc: "f.leone@donders.ru.nl"f.leone@fcdonders.ru.nl, freesurfer@nmr.mgh.harvard.edu Sent: Thursday, November 4, 2010 4:37:34 PM GMT +01:00 Amsterdam / Berlin / Bern / Rome / Stockholm / Vienna Subject: Re: [Freesurfer] Custom color scale for overlays in tksurfer/freeview
You mean even after you adjust the range of the scale, you still can only see a binary-like overlay colors? That seems to be odd.
As to visualize your circular data, you just need a customized color mapping, is that right?
On 11/4/10 11:15 AM, f.leone@donders.ru.nl wrote:
Hi Ruopeng,
Thanks for the answer. Actually, the results I describe are already with changes to the color scale. It is still quite coarse though in my opinion.
Actually have an added wish now: I want to be able to plot circular data in freeview (retinotopic mapping), is this possible?
kind regards, Frank----- Oorspronkelijk bericht ----- Van: "Ruopeng Wang"rpwang@nmr.mgh.harvard.edu Aan: "Frank Leoné"f.leone@donders.ru.nl Cc: "f.leone@donders.ru.nl"f.leone@fcdonders.ru.nl, freesurfer@nmr.mgh.harvard.edu Verzonden: Donderdag 4 november 2010 15:54:14 GMT +01:00 Amsterdam / Berlijn / Bern / Rome / Stockholm / Wenen Onderwerp: Re: [Freesurfer] Custom color scale for overlays in tksurfer/freeview
If you load the data as overlay in freeview, you should be able to adjust the color scale to see the gradient.
On 11/4/10 6:18 AM, f.leone@donders.ru.nl wrote:
Hi everyone,
I saw there has been posts on this before, and I know more people here at the center have this request, so I wanted to ask it again, now also for freeview: is it possible to have custom coloring on the surfaces? It is not that I need specific colors, it is just that I find the default coloring not high resolution enough to see anything more than general level differences (e.g., if I have values 0 to 100, I can only see differences between below or above 60 (red vs yellow, plus there is osme dark red for below 40), while I would like to be able to see the gradient and in between values.
Or isn't this normal behavior? Can it for example be due to using Virtual GL or due to using double precision values? I just tested using integer data (ranging from 0 to 40) and that was a bit better, but still not as good as I would expect.
Anyone any ideas on what I might be doing wrong / whether there is an alternative?
kind regards, FrankThe information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Playing with it some more, I notice the color wheel doesn't work in freeview. Is that true? I did load two maps, sin and cos component, but still the complex options are grayed out. Hoped that might improve the representation.
Thanks,
Frank
----- Original Message ----- From: "Ruopeng Wang" rpwang@nmr.mgh.harvard.edu To: "Frank Leoné" f.leone@donders.ru.nl Cc: "f.leone@donders.ru.nl" f.leone@fcdonders.ru.nl, freesurfer@nmr.mgh.harvard.edu Sent: Thursday, November 4, 2010 4:37:34 PM GMT +01:00 Amsterdam / Berlin / Bern / Rome / Stockholm / Vienna Subject: Re: [Freesurfer] Custom color scale for overlays in tksurfer/freeview
You mean even after you adjust the range of the scale, you still can only see a binary-like overlay colors? That seems to be odd.
As to visualize your circular data, you just need a customized color mapping, is that right?
On 11/4/10 11:15 AM, f.leone@donders.ru.nl wrote:
Hi Ruopeng,
Thanks for the answer. Actually, the results I describe are already with changes to the color scale. It is still quite coarse though in my opinion.
Actually have an added wish now: I want to be able to plot circular data in freeview (retinotopic mapping), is this possible?
kind regards, Frank----- Oorspronkelijk bericht ----- Van: "Ruopeng Wang"rpwang@nmr.mgh.harvard.edu Aan: "Frank Leoné"f.leone@donders.ru.nl Cc: "f.leone@donders.ru.nl"f.leone@fcdonders.ru.nl, freesurfer@nmr.mgh.harvard.edu Verzonden: Donderdag 4 november 2010 15:54:14 GMT +01:00 Amsterdam / Berlijn / Bern / Rome / Stockholm / Wenen Onderwerp: Re: [Freesurfer] Custom color scale for overlays in tksurfer/freeview
If you load the data as overlay in freeview, you should be able to adjust the color scale to see the gradient.
On 11/4/10 6:18 AM, f.leone@donders.ru.nl wrote:
Hi everyone,
I saw there has been posts on this before, and I know more people here at the center have this request, so I wanted to ask it again, now also for freeview: is it possible to have custom coloring on the surfaces? It is not that I need specific colors, it is just that I find the default coloring not high resolution enough to see anything more than general level differences (e.g., if I have values 0 to 100, I can only see differences between below or above 60 (red vs yellow, plus there is osme dark red for below 40), while I would like to be able to see the gradient and in between values.
Or isn't this normal behavior? Can it for example be due to using Virtual GL or due to using double precision values? I just tested using integer data (ranging from 0 to 40) and that was a bit better, but still not as good as I would expect.
Anyone any ideas on what I might be doing wrong / whether there is an alternative?
kind regards, FrankThe information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
The complex color options were just placeholders and never implemented. They will be in the next release (not the one targeted by the end of the month).
On 11/6/10 7:20 AM, f.leone@donders.ru.nl wrote:
Playing with it some more, I notice the color wheel doesn't work in freeview. Is that true? I did load two maps, sin and cos component, but still the complex options are grayed out. Hoped that might improve the representation.
Thanks,
Frank----- Original Message ----- From: "Ruopeng Wang"rpwang@nmr.mgh.harvard.edu To: "Frank Leoné"f.leone@donders.ru.nl Cc: "f.leone@donders.ru.nl"f.leone@fcdonders.ru.nl, freesurfer@nmr.mgh.harvard.edu Sent: Thursday, November 4, 2010 4:37:34 PM GMT +01:00 Amsterdam / Berlin / Bern / Rome / Stockholm / Vienna Subject: Re: [Freesurfer] Custom color scale for overlays in tksurfer/freeview
You mean even after you adjust the range of the scale, you still can only see a binary-like overlay colors? That seems to be odd.
As to visualize your circular data, you just need a customized color mapping, is that right?
On 11/4/10 11:15 AM, f.leone@donders.ru.nl wrote:
Hi Ruopeng,
Thanks for the answer. Actually, the results I describe are already with changes to the color scale. It is still quite coarse though in my opinion.
Actually have an added wish now: I want to be able to plot circular data in freeview (retinotopic mapping), is this possible?
kind regards, Frank----- Oorspronkelijk bericht ----- Van: "Ruopeng Wang"rpwang@nmr.mgh.harvard.edu Aan: "Frank Leoné"f.leone@donders.ru.nl Cc: "f.leone@donders.ru.nl"f.leone@fcdonders.ru.nl, freesurfer@nmr.mgh.harvard.edu Verzonden: Donderdag 4 november 2010 15:54:14 GMT +01:00 Amsterdam / Berlijn / Bern / Rome / Stockholm / Wenen Onderwerp: Re: [Freesurfer] Custom color scale for overlays in tksurfer/freeview
If you load the data as overlay in freeview, you should be able to adjust the color scale to see the gradient.
On 11/4/10 6:18 AM, f.leone@donders.ru.nl wrote:
Hi everyone,
I saw there has been posts on this before, and I know more people here at the center have this request, so I wanted to ask it again, now also for freeview: is it possible to have custom coloring on the surfaces? It is not that I need specific colors, it is just that I find the default coloring not high resolution enough to see anything more than general level differences (e.g., if I have values 0 to 100, I can only see differences between below or above 60 (red vs yellow, plus there is osme dark red for below 40), while I would like to be able to see the gradient and in between values.
Or isn't this normal behavior? Can it for example be due to using Virtual GL or due to using double precision values? I just tested using integer data (ranging from 0 to 40) and that was a bit better, but still not as good as I would expect.
Anyone any ideas on what I might be doing wrong / whether there is an alternative?
kind regards, FrankThe information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
freesurfer@nmr.mgh.harvard.edu
-
f.leone＠donders.ru.nl -
Ruopeng Wang