Gain ref different size than tifs

[cgisriel]

Hello, I recently collected a data set and upon attempting motion correction, I get the error below. The physical pixel size is 0.825 for the tifs, but in the header of the gain reference, I see that the superresolution pixel size is 0.429 (rather than the expected 0.4125 which is half of 0.825). When I look at the gain reference and a micrograph image in imod, I can see that they are different sizes by a factor of two (see attached image). How can I correct the gain reference?

Here is the full error message:

fn_mic: tifs/FoilHole_29283866_Data_29284692_29284694_20240229_120829_fractions.tiff nx = 5760 ny = 4092 gain nx = 11520 gain ny = 8184
in: /dev/shm/ms725/build/RELION/3.1.4/fosscuda-2020b/relion-3.1.4/src/motioncorr_runner.cpp, line 1065
ERROR:
The size of the image and the size of the gain reference do not match. Make sure the gain reference has been rotated if necessary.
=== Backtrace ===
/vast/palmer/apps/avx2/software/RELION/3.1.4-fosscuda-2020b/bin/relion_run_motioncorr(_ZN11RelionErrorC1ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES7_l+0x63) [0x4cf463]
/vast/palmer/apps/avx2/software/RELION/3.1.4-fosscuda-2020b/bin/relion_run_motioncorr() [0x44d07e]
/vast/palmer/apps/avx2/software/RELION/3.1.4-fosscuda-2020b/bin/relion_run_motioncorr(_ZN16MotioncorrRunner3runEv+0x3db) [0x512c7b]
/vast/palmer/apps/avx2/software/RELION/3.1.4-fosscuda-2020b/bin/relion_run_motioncorr(main+0x42) [0x4c50f2]
/lib64/libc.so.6(__libc_start_main+0xe5) [0x1471732d0d85]
/vast/palmer/apps/avx2/software/RELION/3.1.4-fosscuda-2020b/bin/relion_run_motioncorr(_start+0x2e) [0x4c7e9e]

ERROR:
The size of the image and the size of the gain reference do not match. Make sure the gain reference has been rotated if necessary.

[cgisriel]

It turns out that the data were accidently not collected in super resolution mode, which explains the problem.

[biochem-fan]

You have to downsample the super-resolution gain reference into the physical size.

You must take harmonic mean, not simple binning or Fourier cropping. This can be done with e2proc2d from EMAN2 but I forgot the command line. If I remember correctly, this was discussed on the CCPEM mailing list before.

Alternatively, you can use relion_estimate_gain to estimate gain from movie frames. Probably this is easier.

[cgisriel]

I was able to make relion_estimate_gain work. Thanks so much for your help!