I keep getting a warning that tells me that the command line options stopped at an input file

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AFNI version info (afni -ver): Caracalla

code text  # or delete if not needed

deepimage:~/Desktop/IMAGES/rm802_20210507> 3dAllineate -final 'wsinc5' -1Dmatrix_apply ./reg/highres_al_mat.aff12.1D -master ./reg/example_func.nii.gz -prefix ./seg/csf2func_temp.nii.gz ./anat/segment_prob_0.nii.gz
++ 3dAllineate: AFNI version=AFNI_24.0.12 (Mar 12 2024) [64-bit]
++ Authored by: Zhark the Registrator
*

> + WARNING: Processing command line options stopped at './anat/segment_prob_0.nii.gz'

++ Source dataset: /home2/gc748/Desktop/IMAGES/rm802_20210507/anat/segment_prob_0.nii.gz
++ Base dataset:   (not given)
++ Loading datasets into memory
 +        -cmass x y z shifts =    0.000    0.000    0.000
 +  shift search range is +/- =   67.410   80.915   86.331
++ OpenMP thread count = 4
++ ========== Applying transformation to 1 sub-bricks ==========
++ wsinc5 interpolation setup:
 +   taper function  = Min sidelobe 3 term
 +   taper cut point = 0.000
 +   window radius   = 5 voxels
 +   window shape    = Cubical
 +   The above can be altered via the AFNI_WSINC5_* environment variables.
 +  (To avoid this message, 'setenv AFNI_WSINC5_SILENT YES'.)
 +   wsinc5 CUBE(5) mask has 1000 points
++ Output dataset ./seg/csf2func_temp.nii.gz
++ 3dAllineate: total CPU time = 0.0 sec  Elapsed = 1.1
++ ###########################################################
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Try using the -input mydset option for your dataset file with 3dAllineate. While some programs will assume dataset filenames as the end will be input, this program prefers these be explicitly specified with "-input" or "-source" options. It seems that it still takes it but just warns you about it.

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Hi!
Thanks so much for this advice! I don't see the warning message anymore and I think you were right in that the initial command was accepted but AFNI still just was warning me. Thanks again!

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