Looking for clarification from the motion correction output

[zhouyi0812]

Hello!
I am a bit confused that after motion correction I have two output as follow:

1. 002C4d7_B2_B5_1_00d00h00m_rig__d1_1152_d2_1536_d3_1_order_F_frames_540.mmap
2. cnmf-memmap_d1_1152_d2_1536_d3_1_order_C_frames_540.mmap
   which one is the correct one that we can use for the following source extraction?
   Thank you!

[EricThomson]

This is something that we just added a discussion for in the most recent release:
https://caiman.readthedocs.io/en/latest/Getting_Started.html#memory-mapping

The C-order one is the one used by CNMF. F-order is optimized for motion correction.

[zhouyi0812]

So after motion correction, I can reload the F order mmap to continue with source extraction if I am using cnmfe?
Thank you!

[EricThomson]

I would recommend follow the demo. See fname_mc (which is F order). Then we resave as fname_new which is C order, which is optimized for CNMF, and what is used for subsequent processing. This is in demo_pipeline_cnmfE.ipynb. I recommend print out those filenames in the notebook and be sure to follow the logic, and the discussion of memory mapping in the docs I just linked to. It can be confusing, and ideally it would be nice to hide all this back-end detail.

I assume you ask because you want to know what you can safely delete, though. In that case, you can delete fname_mc as the file referred to in fname_new is what you want. That is what is linked to in cnmfe_model.mmap_file for instance, and used for cnmf.

[EricThomson]

The new notebooks are up with much more explanation (for instance of corr/pnr).