Re: [Freesurfer] Display results with tksurfer

[Wang, Ruopeng]

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 
mailto:marina.fdez.alva...@gmail.com>> wrote:


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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
 Mon, 19 Oct 2020 07:50:56 
-0700

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:


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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

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Re: [Freesurfer] Display results with tksurfer

[Douglas N. Greve]

Not sure. Ruopeng (cc'ed) can comment on the control of the color bar

On 10/20/2020 5:05 AM, Marina Fernández wrote:


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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 
 
Mon, 19 Oct 2020 07:50:56 -0700 



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

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[Freesurfer] Display results with tksurfer

[Marina Fernández]

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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

 Mon, 19 Oct 2020 07:50:56 -0700

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

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Re: [Freesurfer] display results with tksurfer

[Douglas N. Greve]

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

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[Freesurfer] display results with tksurfer

[Marina Fernández]

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
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