Hello - I am new to this forum and toolset and very grateful for you for putting together this instruction set.  I followed the instructions and was able to install the macro for FIJI (Parallel FIJI CMTK Registration Mac20 on my mac), but I am getting an error with no reformatting (see below for details) even when I use the test dataset linked from the dropbox earlier in this thread.  I have no coding experience, so I think I am the type of person you wrote these instruction for and I'd very much appreciate your help in getting te fly brain registration to work for me.  Thank you so much

result from running macro:

Started Affine and Warp Registration on 1 samples
Preset: Full Flybrain(Cachero-Ostrovksy_2010)
 
Affine parameters:
Initial affine method: --centers-of-mass
Affine registration metric: Normalized Mutual Information
Exploration [Initial optimizer step size]: 16
Accuracy [Final optimizer step size]: 0.8
Degrees of freedom first pass: 6
Degrees of freedom second pass: 9

Warp parameters:
Warp registration metric: Normalized Mutual Information
initial exploration step size: 26
Accuracy [Final exploration step size]: 0.4
coarsest resampling: 8
Refine grid: 4
grid size: 80
 
Job list:
gehirn
(cmtk make_initial_affine --centers-of-mass /Users/meilinwu/Desktop/test/refbrain/JRC2018_UNISEX_20xHR.nrrd /Users/meilinwu/Desktop/test/images/gehirn_01.nrrd /Users/meilinwu/Desktop/test/result/gehirn_Registration_2026-1-13-13-8/gehirn_init.list; cmtk registration --initial /Users/meilinwu/Desktop/test/result/gehirn_Registration_2026-1-13-13-8/gehirn_init.list --nmi --dofs 6 --dofs 9 --nmi --exploration 16 --accuracy 0.8 --omit-original-data -o /Users/meilinwu/Desktop/test/result/gehirn_Registration_2026-1-13-13-8/gehirn_affine.xform /Users/meilinwu/Desktop/test/refbrain/JRC2018_UNISEX_20xHR.nrrd /Users/meilinwu/Desktop/test/images/gehirn_01.nrrd; cmtk warp --nmi --threads 160 --jacobian-weight 0 --fast -e 26 --grid-spacing 80 --energy-weight 1e-1 --refine 4 --coarsest 8 --ic-weight 0 --accuracy 0.4 --omit-original-data -o /Users/meilinwu/Desktop/test/result/gehirn_Registration_2026-1-13-13-8/gehirn_warp.xform /Users/meilinwu/Desktop/test/result/gehirn_Registration_2026-1-13-13-8/gehirn_affine.xform;cd /Users/meilinwu/Desktop/test/result/gehirn_Registration_2026-1-13-13-8; cmtk reformatx --pad-out 0 -o Reformatted/warp_gehirn_01.nrrd --floating /Users/meilinwu/Desktop/test/images/gehirn_01.nrrd /Users/meilinwu/Desktop/test/refbrain/JRC2018_UNISEX_20xHR.nrrd /Users/meilinwu/Desktop/test/result/gehirn_Registration_2026-1-13-13-8/gehirn_warp.xform & cd /Users/meilinwu/Desktop/test/result/gehirn_Registration_2026-1-13-13-8; cmtk reformatx --pad-out 0 -o Reformatted/warp_gehirn_02.nrrd --floating /Users/meilinwu/Desktop/test/images/gehirn_02.nrrd /Users/meilinwu/Desktop/test/refbrain/JRC2018_UNISEX_20xHR.nrrd /Users/meilinwu/Desktop/test/result/gehirn_Registration_2026-1-13-13-8/gehirn_warp.xform & cd /Users/meilinwu/Desktop/test/result/gehirn_Registration_2026-1-13-13-8; cmtk reformatx --pad-out 0 -o Reformatted/warp_gehirn_03.nrrd --floating /Users/meilinwu/Desktop/test/images/gehirn_03.nrrd /Users/meilinwu/Desktop/test/refbrain/JRC2018_UNISEX_20xHR.nrrd /Users/meilinwu/Desktop/test/result/gehirn_Registration_2026-1-13-13-8/gehirn_warp.xform ) & 
 
Please wait
(cmtk make_initial_affine --centers-of-mass /Users/meilinwu/Desktop/test/refbrain/JRC2018_UNISEX_20xHR.nrrd /Users/meilinwu/Desktop/test/images/gehirn_01.nrrd /Users/meilinwu/Desktop/test/result/gehirn_Registration_2026-1-13-13-8/gehirn_init.list; cmtk registration --initial /Users/meilinwu/Desktop/test/result/gehirn_Registration_2026-1-13-13-8/gehirn_init.list --nmi --dofs 6 --dofs 9 --nmi --exploration 16 --accuracy 0.8 --omit-original-data -o /Users/meilinwu/Desktop/test/result/gehirn_Registration_2026-1-13-13-8/gehirn_affine.xform /Users/meilinwu/Desktop/test/refbrain/JRC2018_UNISEX_20xHR.nrrd /Users/meilinwu/Desktop/test/images/gehirn_01.nrrd; cmtk warp --nmi --threads 160 --jacobian-weight 0 --fast -e 26 --grid-spacing 80 --energy-weight 1e-1 --refine 4 --coarsest 8 --ic-weight 0 --accuracy 0.4 --omit-original-data -o /Users/meilinwu/Desktop/test/result/gehirn_Registration_2026-1-13-13-8/gehirn_warp.xform /Users/meilinwu/Desktop/test/result/gehirn_Registration_2026-1-13-13-8/gehirn_affine.xform;cd /Users/meilinwu/Desktop/test/result/gehirn_Registration_2026-1-13-13-8; cmtk reformatx --pad-out 0 -o Reformatted/warp_gehirn_01.nrrd --floating /Users/meilinwu/Desktop/test/images/gehirn_01.nrrd /Users/meilinwu/Desktop/test/refbrain/JRC2018_UNISEX_20xHR.nrrd /Users/meilinwu/Desktop/test/result/gehirn_Registration_2026-1-13-13-8/gehirn_warp.xform & cd /Users/meilinwu/Desktop/test/result/gehirn_Registration_2026-1-13-13-8; cmtk reformatx --pad-out 0 -o Reformatted/warp_gehirn_02.nrrd --floating /Users/meilinwu/Desktop/test/images/gehirn_02.nrrd /Users/meilinwu/Desktop/test/refbrain/JRC2018_UNISEX_20xHR.nrrd /Users/meilinwu/Desktop/test/result/gehirn_Registration_2026-1-13-13-8/gehirn_warp.xform & cd /Users/meilinwu/Desktop/test/result/gehirn_Registration_2026-1-13-13-8; cmtk reformatx --pad-out 0 -o Reformatted/warp_gehirn_03.nrrd --floating /Users/meilinwu/Desktop/test/images/gehirn_03.nrrd /Users/meilinwu/Desktop/test/refbrain/JRC2018_UNISEX_20xHR.nrrd /Users/meilinwu/Desktop/test/result/gehirn_Registration_2026-1-13-13-8/gehirn_warp.xform ) &  wait;
execution time was 0 s.
 
gehirn Registration warp failed
gehirn Registration affine failed
Reformat failed:/Users/meilinwu/Desktop/test/result/gehirn_Registration_2026-1-13-13-8/Reformatted/warp_gehirn_01.nrrd
Reformat failed:/Users/meilinwu/Desktop/test/result/gehirn_Registration_2026-1-13-13-8/Reformatted/warp_gehirn_02.nrrd
Reformat failed:/Users/meilinwu/Desktop/test/result/gehirn_Registration_2026-1-13-13-8/Reformatted/warp_gehirn_03.nrrd
 
Reformatted 0 images