import IMOD files into Relion5

[ariel234156]

Hello,
I tried running AlignTiltSeries manually in batchruntomo with RAPTOR and got a very good tomogram. But when I tried to enter the alignment files into the AlignTiltSeries job, the tomogram that the relion built was terrible. This means the way the relion uses the Xf file differs from direct IMOD reconstruction.
Is there another transformation between regular batchruntomo and when I run it from relion?
There are no errors in the pipeline
The way how I upload the files is:

1. running AlignTiltSeries in relion.
2. replace external IMOD files with my files
3. doing "continue" on the alignment job again (I removed the star files to ensure the relion writes new from the new files)
4. reconstruct the tomogram in relion.
   Thank you.