afni.nimh.nih.gov

Hi, Daniel
Thanks for your reply!. I did try to avoid the skull-stripping step. I cleaned up my cmd a little bit. As you can see, I set '-dset1_strp None -dset2_strip None'

align_epi_anat.py -dset1 dset.nii.gz -dset2 dset2.nii.gz -master_dset2 dset2.nii.gz -suffix _al.nii.gz -dset1to2 -output_dir outputdir -giant_move -dset1_strip None -dset2_strip None -overwrite -rigid_body -Allineate_opts -weight dset2_brainmask.nii.gz

But it still internally add a -weight input. Did I miss something?

#Script is running (command trimmed):
3dAllineate -lpa -wtprefix ./__tt_dset2.nii.gz_wtal -weight ./__tt_dset1_ts_wt+orig -source ./__tt_dset2 -prefix ./dset1.nii.gz -base ./__tt_dset2_ts+orig -cmass -1Dmatrix_save ./dset2_al.nii.gz_mat.aff12.1D -master BASE -mast_dxyz 0.500000 -weight ./dset1_brainmask.nii.gz -twobest 11 -twopass -VERB -maxrot 45 -maxshf 40 -fineblur 1
-source_automask+2
++ 3dAllineate: AFNI version=AFNI_18.2.19 (Sep 27 2018) [64-bit]
++ Authored by: Zhark the Registrator
*+ WARNING: Small value 0.5 after -mast_dxyz
** FATAL ERROR: Can't have multiple -weight options
** Program compile date = Sep 27 2018
** 3dAllineate failure
** ERROR - script failed


thanks.

ruyuan