Hi, Angelika-

Indeed, your input EPI should be in native space, not a standard space, before processing starts.

There are 2 ways it might *appear* to be in standard space:
1) It *is* actually in standard space.
2) It is a NIFTI file, and it has an qform_code and/or sform_code value in its header that is the dreaded "ambiguous space" one that was somehow allowed in the NIFTI standard. From here, we can see what allowed [qs]form_code values there are (and a new one exists now, code=5, which represents "other" templates than those in code=3,4):

Name 	Code 	Description
unknown 	0 	Arbitrary coordinates. Use Method 1.
scanner_anat 	1 	Scanner-based anatomical coordinates.
aligned_anat 	2 	Coordinates aligned to another file, or to the “truth” (with an arbitrary coordinate center).
talairach 	3 	Coordinates aligned to the Talairach space.
mni_152 	4 	Coordinates aligned to the mni space.

The dreaded ambiguous coding is code=2; if your NIFTI dataset has that, AFNI has to choose whether to consider that in 'original' or 'standard' space, which is controlled with an environment variable AFNI_NIFTI_VIEW.

So, first let's check what the [qs]form_code values are in your dataset, to see if we are in case #1 or case #2 from above. What is the output of the following, where DSET_EPI is your input EPI time series dataset (/group/.../1002002_V001_DMSRun1.nii)?

nifti_tool -disp_hdr -field qform_code -field sform_code -infiles DSET_EPI

--pt

ps: for reference, here is your afni_proc.py command spaced out, ~one option per line:

afni_proc.py                                                                 \
    -subj_id                  1002002                                        \
    -out_dir                  /group/.../1002002_processed                   \
    -script                   /home/.../scriptss/1002002/1002002             \
    -scr_overwrite                                                           \
    -dsets                    /group/.../1002002_V001_DMSRun1.nii            \
    -blocks                   despike tshift align tlrc volreg mask blur     \
                              regress                                        \
    -copy_anat                /group/northoff/share/sswarper_ang/1002002/anatSS.1002002.nii \
    -anat_has_skull           no                                             \
    -align_opts_aea                                                          \
    -cost                     lpc+ZZ                                         \
    -big_move                                                                \
    -volreg_align_e2a                                                        \
    -volreg_align_to          MIN_OUTLIER                                    \
    -volreg_tlrc_warp                                                        \
    -tlrc_base                MNI152_2009_template_SSW.nii.gz                \
    -tlrc_NL_warp                                                            \
    -tlrc_NL_warped_dsets     /group/northoff/share/sswarper_ang/1002002/anatQQ.1002002.nii \
                              /group/northoff/share/sswarper_ang/1002002/anatQQ.1002002.aff12.1D \
                              /group/northoff/share/sswarper_ang/1002002/anatQQ.1002002_WARP.nii \
    -volreg_post_vr_allin     yes                                            \
    -volreg_pvra_base_index   MIN_OUTLIER                                    \
    -mask_segment_anat        yes                                            \
    -mask_segment_erode       yes                                            \
    -regress_anaticor                                                        \
    -regress_ROI              WMe CSFe                                       \
    -regress_apply_mot_types  demean deriv                                   \
    -regress_motion_per_run                                                  \
    -regress_censor_motion    0.25                                           \
    -regress_censor_outliers  0.1                                            \
    -blur_size                6.0                                            \
    -regress_est_blur_epits                                                  \
    -regress_est_blur_errts                                                  \
    -html_review_style        pythonic                                       \
    -execute