Dear Emilie,

I have been working on my issue and managed to get the file intermediate_processing being created! It is saved directly on the path studydir, so the file is created in the same place as 2dseq is (that means C:\Users\Katka\Desktop\sikorova\20200803_140853_celer_1_1\19\pdata\1) - this folder contains also the id, method, procs, reco, roi and visu_pars files from bruker.

The file intermediate_processing contains these sub folders: dki_avg1_coreg, dki_avg1_nii, dki_b0_coreg, dki_b0_nii, but it did not come to the successful ending, because there was an error which stopped the process:

Error using nifti/create>create_each (line 29)
Unable to write header for
"C:\Users\Katka\Desktop\sikorova\20200803_140853_celer_1_1\19\pdata\1\intermediate_processing\dki_avg2_nii\adki_300.nii".

Error in nifti/create (line 15)
Error in spm_create_vol>create_vol (line 162)
Error in spm_create_vol (line 16)
Error in spm_write_vol (line 82)
Error in dke_preprocess_bruker>image_avg (line 294)
Error in dke_preprocess_bruker (line 109)
Error in dke (line 176)

So apparently it is supposed to create more subfolders, but something caused the early stopping - I do not understand why the first four folders with files could have been created without any problem, but then the DKE was unable write header and so on...

Best regards,
Pavlína