users > RE: Failed to register one plane's calcium imaging trace onto template
Jan 21, 2021  10:01 PM | Greg Jefferis
RE: Failed to register one plane's calcium imaging trace onto template
I can only give you some rough guidance, but I would do as follows

1. average each time series calcium recording over time reducing 4D->3D stack
2. register the 3D average stack to that fish's anatomical stack
3. register fish's anatomical stack to the template

now you have two 3D -> 3D registrations that link the 3D space of your time series data to your template. You now have two options

1. transform your time series data to the template
2. transform the template to your time series data

2 is actually much easier if your goal is to see e.g. how calcium activity lines up with 3D anatomical regions.
I only know how to do 1 by splitting up the time points and writing separate files for each (script in imageJ?)

To apply this the command line would look something like:

1. reformat --floating calcium-timepoint.nii template.nii reg1 reg2
2. reformat --floating template.nii calcium-avg.nii -- --inverse reg2 --inverse reg1
[or compute the registrations in the opposite direction]

There are fancier variations to deal with movement in the initial time series if this is an issue. I would be very happy to hear advice from anyone else who has processed functional image data.

Best, Greg.

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TitleAuthorDate
Yuxin Tong Jan 21, 2021
Kevin Mann Jan 22, 2021
Greg Jefferis Jan 23, 2021
RE: Failed to register one plane's calcium imaging trace onto template
Greg Jefferis Jan 21, 2021
Yuxin Tong Jan 21, 2021