External Email - Use Caution
Thanks for the reply Doug,
We used the tksurfer command lines because they were run in matlab after performing some analysis to obtain the figures of the results. With the scripts, these figures are automatically saved for later review. We would like to know if what you propose with freeview is appropriate for this and if we can modify the scale of min-max significant t values with the freeview options (I copy the previous message below).
Thank you so much for your attention.
Best regards, Marina
-------------------------------------------------------------------------------------------------------------------------------
Douglas N. Greve https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from:%22Douglas+N.+Greve%22 Mon, 19 Oct 2020 07:50:56 -0700 https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date:20201019 Not sure, we don't use tksurfer that much anymore. Have you tried freeview? You can run freeview with tksurferfv and the same tksurfer arguments (makes it easier)
On 10/13/2020 5:03 AM, Marina Fernández wrote:
External Email - Use Caution
Dear Freesurfer experts,
I would like to modify the values of the colorbar scale to display results in the inflated surface with tksurfer, in such a way that displayed values in the colorbar range from the minimum t- value detected to the maximum t value detected. I have tried to use the -fminmax flag, but the colorbar scale shows values from 0 to the maximum t value. Is it possible to limit values of the colorbar scale to min-max significant t values?
On the other hand, is it possible to invert the colors of the colorbar scale (e.g., red for higher t values and yellow for lower t values)?
Thank you in advance.
Best regards, Marina
_______________________________________________ Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Not sure. Ruopeng (cc'ed) can comment on the control of the color bar
On 10/20/2020 5:05 AM, Marina Fernández wrote:
External Email - Use Caution
Thanks for the reply Doug,
We used the tksurfer command lines because they were run in matlab after performing some analysis to obtain the figures of the results. With the scripts, these figures are automatically saved for later review. We would like to know if what you propose with freeview is appropriate for this and if we can modify the scale of min-max significant t values with the freeview options (I copy the previous message below).
Thank you so much for your attention.
Best regards, Marina
Douglas N. Greve https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from:%22Douglas+N.+Greve%22 Mon, 19 Oct 2020 07:50:56 -0700 https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date:20201019
Not sure, we don't use tksurfer that much anymore. Have you tried freeview? You can run freeview with tksurferfv and the same tksurfer arguments (makes it easier)
On 10/13/2020 5:03 AM, Marina Fernández wrote:
External Email - Use Caution Dear Freesurfer experts, I would like to modify the values of the colorbar scale to display results in the inflated surface with tksurfer, in such a way that displayed values in the colorbar range from the minimum t- value detected to the maximum t value detected. I have tried to use the -fminmax flag, but the colorbar scale shows values from 0 to the maximum t value. Is it possible to limit values of the colorbar scale to min-max significant t values?On the other hand, is it possible to invert the colors of the colorbar scale (e.g., red for higher t values and yellow for lower t values)? Thank you in advance. Best regards, Marina _______________________________________________ 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
Hi Marina,
If you meant to set threshold for surface overlay from the command-line, you can do it like this:
freeview -f lh.inflated:overlay=overlay_file:overlay_threshold=min,max
For more overlay options, you can run ‘freeview -h’ and look under ‘-f, --surface’ section.
Best, Ruopeng
On Oct 20, 2020, at 5:05 AM, Marina Fernández <marina.fdez.alvarez@gmail.commailto:marina.fdez.alvarez@gmail.com> wrote:
External Email - Use Caution
Thanks for the reply Doug,
We used the tksurfer command lines because they were run in matlab after performing some analysis to obtain the figures of the results. With the scripts, these figures are automatically saved for later review. We would like to know if what you propose with freeview is appropriate for this and if we can modify the scale of min-max significant t values with the freeview options (I copy the previous message below).
Thank you so much for your attention.
Best regards, Marina
-------------------------------------------------------------------------------------------------------------------------------
Douglas N. Grevehttps://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from:%22Douglas+N.+Greve%22 Mon, 19 Oct 2020 07:50:56 -0700https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date:20201019
Not sure, we don't use tksurfer that much anymore. Have you tried freeview? You can run freeview with tksurferfv and the same tksurfer arguments (makes it easier)
On 10/13/2020 5:03 AM, Marina Fernández wrote:
External Email - Use Caution
Dear Freesurfer experts,
I would like to modify the values of the colorbar scale to display results in the inflated surface with tksurfer, in such a way that displayed values in the colorbar range from the minimum t- value detected to the maximum t value detected. I have tried to use the -fminmax flag, but the colorbar scale shows values from 0 to the maximum t value. Is it possible to limit values of the colorbar scale to min-max significant t values?
On the other hand, is it possible to invert the colors of the colorbar scale (e.g., red for higher t values and yellow for lower t values)?
Thank you in advance.
Best regards, Marina
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Douglas N. Greve -
Marina Fernández -
Wang, Ruopeng