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Question about Retinotopy program #7

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resungod opened this issue Mar 3, 2016 · 6 comments
Open

Question about Retinotopy program #7

resungod opened this issue Mar 3, 2016 · 6 comments

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@resungod
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resungod commented Mar 3, 2016

Hi Vistalab,

We downloaded the code (i.e., vistadisp-master.zip) and used the Retinotopy program a long while ago.

(1) Recently, we found that the "retinotopy" GUI is updated with new parameter setting (for example, there are new menu, STIM sppearance and Load/Save box, compared with previous GUI). We do not know what the parameters means.

size(deg): contrast motion steps temp freq

<Load/Save box>
For "Load image matrix", we used "gak_8bars.mat", but we cannot find the choosing option in the GUI.

(2) For "load display information" in GUI, we do not know which one we have to choose.
We are using the BOLD screen resolution is 1280x1024 (made by Cambridge Research (not a common desktop monitor manufacturer)). Here is a link to the specs on their site: http://www.crsltd.com/tools-for-functional-imaging/mr-safe-displays/boldscreen-3d-lcd-for-fmri/nest/boldscreen-3d-technical-specification#npm

For better understanding of above 2 questions, I attached our previous GUI parameter setting image (retMenu_old) and current GUI parameter image (retMenu_current).

<retMenu_old>
retmenu_old

<retMenu_current>
retmenu_current

Thank you.
@JWinawer
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JWinawer commented Mar 5, 2016

(1)

"size (deg)" is the stimulus extent in degrees of visual angle.
"Contrast" is the stimulus contrast of the stimulus (Michelson contrast, I
think).
"Motion steps" is the number of checkerboard positions per luminance cycle
"tempFreq" is the temporal frequency of the drifting contrast pattern

For "load image matrix", the image matrix must be in the folder,
vistadisp/Applications2/Retinotopy/standard/storedImagesMatrices/

To better understand what the parameters do, I suggest that you run a few
example experiments from the command line. For example:

params = retCreateDefaultGUIParams;
params.contrast = .3;
params.stimSize = 2;
params.prescanDuration = 0;
ret(params)

(2)
For calibration, I would suggest you calibrate your display and add the
appropriate files to your vistadisp path. For an example, see
vistadisp/exptTools2/displays/CBI_NYU_projector

There is some information on display calibrations on the Wandell lab
software page for calibrations that include spectra (color)
http://web.stanford.edu/group/vista/cgi-bin/wiki/index.php/Stimulus#Calibrating_a_display

There is some information on my lab's wiki page for calibrating luminance
only:
https://wikis.nyu.edu/display/winawerlab/Monitor+Calibration

-JW

On Thu, Mar 3, 2016 at 3:44 PM, resungod [email protected] wrote:

Hi Vistalab,

We downloaded the code (i.e., vistadisp-master.zip) and used the
Retinotopy program a long while ago.

(1) Recently, we found that the "retinotopy" GUI is updated with new
parameter setting (for example, there are new menu, STIM appearance and
Load/Save box, compared with previous GUI). We do not know what the
parameters means.

size(deg): contrast
motion steps temp freq

For "Load image matrix", we used "gak_8bars.mat", but we cannot find the
choosing option in the GUI.

(2) For "load display information" in GUI, we do not know which one we
have to choose.
We are using the BOLD screen resolution is 1280x1024 (made by Cambridge
Research (not a common desktop monitor manufacturer)). Here is a link to
the specs on their site:
http://www.crsltd.com/tools-for-functional-imaging/mr-safe-displays/boldscreen-3d-lcd-for-fmri/nest/boldscreen-3d-technical-specification#npm

For better understanding of above 2 questions, I attached our previous GUI
parameter setting image (retMenu_old) and current GUI parameter image
(retMenu_current).

[image: retmenu_old]
https://cloud.githubusercontent.com/assets/17624055/13508854/5ad3d044-e14e-11e5-95f3-6eaf603b7581.png

[image: retmenu_current]
https://cloud.githubusercontent.com/assets/17624055/13508850/58516ed0-e14e-11e5-81a9-637662d9cafc.png

Thank you.

—
Reply to this email directly or view it on GitHub
#7.

Jonathan Winawer
Assistant Professor of Psychology and Neural Science

New York University
6 Washington Place
New York, NY, 10003
(212) 998-7922 (phone)
(212) 995-4018 (fax)
[email protected]
http://psych.nyu.edu/winawer/

@resungod
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Hi Vistalab,
Thank you so much for your comments. The above comments were very helpful to understand the GUI parameter setting environment.

Could I ask one more question?

When I run the Retinotopy program using MATLAB version 2013b, it works well like below:
ret_menu

When I run the Retinotopy program using MATLAB version 2014b/2015a, several GUI box are missing like below:
ret_nodisplay

Is this reason because of different MATLAB version or because of other issue?
Please let me know.

Thank you so much again for your help.

Best,

@JWinawer
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Yes, this is a Matlab version issue, which should be fixed. In the
meantime, you can fully control all parameters from the command line (or
from the GUI using an older version of Matlab).

On Tue, Mar 15, 2016 at 3:01 PM, resungod [email protected] wrote:

Hi Vistalab,
Thank you so much for your comments. The above comments were very helpful
to understand the GUI parameter setting environment.

Could I ask one more question?

When I run the Retinotopy program using MATLAB version 2013b, it works
well like below:
[image: ret_menu]
https://cloud.githubusercontent.com/assets/17624055/13790356/0a21e732-eab6-11e5-94fe-e2548cfb8f93.jpg

When I run the Retinotopy program using MATLAB version 2014b/2015a,
several GUI box are missing like below:
[image: ret_nodisplay]
https://cloud.githubusercontent.com/assets/17624055/13790404/471237a0-eab6-11e5-863a-c744cafa0e09.jpg

Is this reason because of different MATLAB version or because of other
issue?
Please let me know.

Thank you so much again for your help.

Best,

—
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Reply to this email directly or view it on GitHub
#7 (comment)

Jonathan Winawer
Assistant Professor of Psychology and Neural Science

New York University
6 Washington Place
New York, NY, 10003
(212) 998-7922 (phone)
(212) 995-4018 (fax)
[email protected]
http://psych.nyu.edu/winawer/

@resungod
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Hi Vistalab,

Thank you so much for your feedback.
Have a great day!

Best,

@marco-create
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Dear Jonathan Winawer,
My name is Marco.
I am responding on this thread because it's showing the exact issue I'm facing. The GUI for newest MATLAB versions, seems still lacking in some parts (MATLAB 2018b).

Am I able to control all parameters only from command line or maybe it has been fixed in some ways that I've missed?

Thank you for your help,
Marco

@JWinawer
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JWinawer commented Oct 15, 2019 via email

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