How to run pipeline on acquisition/ subject class

[VeroniqueChouinard]

Hello Bruno, how are you?

I saw that the toolbox integrates the possibility on running the pipeline on the acquisition class and subject as well. I would like to try running the pipeline on the acquisition class instead of modality like I usually do but i don't know how to go about it.
To be precise, my idea is to produce an average map of multiple acquisitions merged together. I do tactile stimulation of the forelimb, hindlimb and whiskers and I would like to be able to produce images of these three or four acquisitions together.

Is there a documentation or examples available to do that?

[BrunoOFSouza]

Hi Veronique,

If I understood correctly, you want to create an average of the activation maps from different acquisitions of a given mouse. There is a way to do it by using a combination of existing functions and tools inside the umIToolbox app.

*The following workflow assumes that the data was already preprocessed and aligned

Here is a workflow that could work for you:

1. Create the amplitude map for each acquisition using the calculate_response_amplitude function.
2. Save the amplitude maps in .mat file format using the function transformDat2Mat. This will allow you to visualize the maps in the Analysis tab of the umIToolbox app.
3. In the Analysis tab, select all recordings that you want to average, select the files containing the maps and click on the Select button (doc).
4. Now, use the utility Avg. Acquisitions to average all maps.
5. Finally, launch the Plot Average Maps to visualize.

Let us know if this doesn't work.

[VeroniqueChouinard]

Thank you, it works perfectly! However, I noticed that in the analysis tab when I select another file by mistake (which I do lot more than I should), Matlab sends the following error :

Error using umIToolbox/SelectFileListBox_analysisValueChanged
'obsID' does not exist in 'F:\BlindMouse_Project2024\Data\Processed\4ADG\iso-stim-lFL-bs-1-3\CtxImg\data_splitByEvent.mat'.

The toolbox then remains in 'please wait' mode until I close it. It's not a huge problem for me since I just have to close and reopen the GUI, but i thought I should still report the bug.

[BrunoOFSouza]

Looks like a Bug. Which version of the toolbox are you using?

Thanks!

[VeroniqueChouinard]

Bipolar- v2.0.0