Author Topic: msRun Error  (Read 2552 times)

kyuhyun

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msRun Error
« on: February 28, 2018, 06:44:49 PM »
Hi,
I've been trying to do analysis through the pipeline. And after aligning, the error message is keeping popped up. I am pretty newbie in the Matlab, so I couldn't make any change with this error.

>> msRun
Calculating column correction. 12.5313% done
Calculating column correction. 75.1876% done
Calculating fluorescence properties: 25% done.
Calculating fluorescence properties: 50% done.
Calculating fluorescence properties: 75% done.
Use mouse to select threshold for mean good fluorescence value
Keep selection? (Y/N)y
Select ROI #1
Select another ROI? (Y/N)Y
Select ROI #2
Select another ROI? (Y/N)N
Alignment 1/2
Calculating shift between frames. On frame 1000
Calculating shift between frames. On frame 2000
Calculating shift between frames. On frame 3000
Alignment 2/2
Calculating shift between frames. On frame 1000
Calculating shift between frames. On frame 2000
Calculating shift between frames. On frame 3000
Elapsed time is 795.770971 seconds.
Select best alignment (Enter number):1
Reading video into memory. 12.5313% done
Reading video into memory. 75.1876% done
Could not find bounds
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Extracting dF/F traces: 5.0025
Extracting dF/F traces: 10.005
Extracting dF/F traces: 15.0075
Extracting dF/F traces: 20.01
Extracting dF/F traces: 25.0125
Extracting dF/F traces: 30.015
Extracting dF/F traces: 35.0175
Extracting dF/F traces: 40.02
Extracting dF/F traces: 45.0225
Extracting dF/F traces: 50.025
Extracting dF/F traces: 55.0275
Extracting dF/F traces: 60.03
Extracting dF/F traces: 65.0325
Extracting dF/F traces: 70.035
Extracting dF/F traces: 75.0375
Extracting dF/F traces: 80.04
Extracting dF/F traces: 85.0425
Extracting dF/F traces: 90.045
Extracting dF/F traces: 95.0475
Reference to non-existent field 'vidObj'.

Error in msGenerateVideoObj (line 33)
    ms.height = ms.vidObj{1}.Height;

Error in msRun (line 78)
behav = msGenerateVideoObj(pwd,'behavCam');
 
>>



How can we fix this?
« Last Edit: February 28, 2018, 07:09:08 PM by kyuhyun »

Daniel Aharoni

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Re: msRun Error
« Reply #1 on: February 28, 2018, 09:45:50 PM »
Hi Kyuhyun,
It looks like the error is coming up when you try and process the behavior video. Did you record behavior on a separate webcam in this recording session?

I would recommend moving away from the old analysis code on my GitHub and instead working with the CaImAn package, https://github.com/flatironinstitute/CaImAn.

kyuhyun

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Re: msRun Error
« Reply #2 on: March 01, 2018, 03:15:17 AM »
I would love to try that. Thanks! :)