size of activation

[evernerve]

Hi
First of all i want to thank you for your efforts to improve this valuable toolbox.
i wanted to know if its possible to measure the size of a specific area in the brain that responds to visual stimuli for example v1 or other area with umit if its possible What will be the pipeline that i need?
best regards

[BrunoOFSouza]

Hi @evernerve,

It is possible to measure the area of a brain region activated by a stimulus. In brief, you can load the brain activation map (fig 1) to the ROImanager app and create an ROI corresponding to the activated area. You can use the option Create >> From threshold... to use a threshold value to delimit the ROI (figs 2-3).
To get the area in mm², you will need the pixel ratio of the recording in pixels per mm. In the ROImanager, go to Image >> Set pixel size and enter the pixel value. Otherwise the app will give the area in pixel².
The area value will be displayed in the table (fig 4).

1. Activation map:
   
2. Create the ROI:
   
3. ROI created!
   
4. Get the ROI area:
   

[DevilsAdvocate2244]

thanks a lot but for pixel ratio What would be the suitable number?

[BrunoOFSouza]

Well, the pixel ratio will give the number of pixels per millimeters in order to be able to estimate the real size of the image. This can vary depending on the zoom (on the lenses) that you used during the recordings. If you always used the same parameters, what you can do is to take a snapshot of an object with known dimensions (e.g. a ruler) and measure the number of pixels per distance.

[DevilsAdvocate2244]

okay thank you Bruno. khodafez

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________________________________ From: BrunoOFSouza ***@***.***> Sent: Thursday, April 20, 2023 10:54 AM To: LabeoTech/Umit ***@***.***> Cc: Hossein Sedighi ***@***.***>; Comment ***@***.***> Subject: Re: [LabeoTech/Umit] size of activation (Discussion #58) Well, the pixel ratio will give the number of pixels per millimeters in order to be able to estimate the real size of the image. This can vary depending on the zoom (on the lenses) that you used during the recordings. If you always used the same parameters, what you can do is to take a snapshot of an object with known dimensions (e.g. a ruler) and measure the number of pixels per distance. — Reply to this email directly, view it on GitHub<#58 (reply in thread)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/A7KLAVQ23JQBBGKMZGQZTV3XCFEZRANCNFSM6AAAAAAWV2ORMM>. You are receiving this because you commented.Message ID: ***@***.***>

[DevilsAdvocate2244]

Another question for threshold level what does it represent?

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________________________________ From: Hossein Sedighi ***@***.***> Sent: Thursday, April 20, 2023 10:56 AM To: LabeoTech/Umit ***@***.***> Subject: Re: [LabeoTech/Umit] size of activation (Discussion #58) okay thank you Bruno. khodafez

________________________________ From: BrunoOFSouza ***@***.***> Sent: Thursday, April 20, 2023 10:54 AM To: LabeoTech/Umit ***@***.***> Cc: Hossein Sedighi ***@***.***>; Comment ***@***.***> Subject: Re: [LabeoTech/Umit] size of activation (Discussion #58) Well, the pixel ratio will give the number of pixels per millimeters in order to be able to estimate the real size of the image. This can vary depending on the zoom (on the lenses) that you used during the recordings. If you always used the same parameters, what you can do is to take a snapshot of an object with known dimensions (e.g. a ruler) and measure the number of pixels per distance. — Reply to this email directly, view it on GitHub<#58 (reply in thread)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/A7KLAVQ23JQBBGKMZGQZTV3XCFEZRANCNFSM6AAAAAAWV2ORMM>. You are receiving this because you commented.Message ID: ***@***.***>

[BrunoOFSouza]

The threshold represents the cut-off value (in pixel value if not normalized or 0-1 if normalized) that will be used to create the ROI.
In the example above, the normalized threshold of 0.4 means that the ROI encompasses an area where all pixel values are below 40% of all pixel values in the image.

There are several ways to determine a threshold. Some more biased than others. The current option is a manual threshold.
I am currently working on the Auto Set button to set the threshold automatically based on the image statistics. But this will only be available on the next version of the toolbox.

For a description of the app's interface elements, check the app`s documentation here.

[DevilsAdvocate2244]

Yes it will be a great help. I think it will be okay after your guidance.