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ENH: Fix header printing#1912

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cookpa merged 5 commits intomasterfrom
fix_matrix_header_print
Oct 7, 2025
Merged

ENH: Fix header printing#1912
cookpa merged 5 commits intomasterfrom
fix_matrix_header_print

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@cookpa cookpa commented Oct 2, 2025

Print matrices and vectors, remove redundant info

Fixes #960

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cookpa commented Oct 2, 2025

I took the orientation code logic from c3d, making clear that the codes (LPI, etc) are FROM orientations, rather than "to" orientations. Nibabel uses the signifier +, RAS+ means increasing towards Right, Anterior, Superior.

In ITK 6.0, the spatial orientation enums are replaced by a new class itkAnatomicalOrientation, which uses unambiguous terms like "RightToLeft" but can also provide the traditional three letter codes.

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gdevenyi commented Oct 2, 2025

Can you post a diff of the output of PrintHeader before and after for a file here?

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cookpa commented Oct 2, 2025

Old is on the left

Spacing [1, 1, 1]					      <	
Origin [96, 132, -78]					      <	
Direction 						      <	
-1 0 0							      <	
0 -1 0							      <	
0 0 1							      <	
   							
Size : 193 229  193					      <	
   						      <	
 Image Dimensions   : [193, 229, 193]				  Image Dimensions   : [193, 229, 193]
 Bounding Box       : {[96 132 -78], [289 361 115]}		  Bounding Box       : {[96 132 -78], [289 361 115]}
   						      >	  Origin             : [96, 132, -78]
 Voxel Spacing      : [1, 1, 1]				  Voxel Spacing      : [1, 1, 1]
 Intensity Range    : [0, 10000]				  Intensity Range    : [0, 10000]
 Mean Intensity     : 2986.67					  Mean Intensity     : 2986.67
   						      >	  Canon. FROM Orient : LPI
 Direction Cos Mtx. : 						  Direction Cos Mtx. : 
-1 0 0							      |	           -1.00000    0.00000    0.00000
0 -1 0							      |	            0.00000   -1.00000    0.00000
0 0 1							      |	            0.00000    0.00000    1.00000
   						      <	
 Voxel->RAS x-form  : 						  Voxel->RAS x-form  : 
   						      >	            1.00000   -0.00000   -0.00000  -96.00000
   						      >	           -0.00000    1.00000   -0.00000 -132.00000
   						      >	            0.00000    0.00000    1.00000  -78.00000
   						      >	            0.00000    0.00000    0.00000    1.00000
 Image Metadata: 						  Image Metadata: 
   ITK_FileNotes = mnc2nii mni_icbm152_nlin_asym_09c/mni_icb	    ITK_FileNotes = mnc2nii mni_icbm152_nlin_asym_09c/mni_icb
   ITK_original_direction of unsupported type N3itk6MatrixId |	    ITK_original_direction =
   ITK_original_spacing of unsupported type NSt3__16vectorId |	           -1.00000   -0.00000   -0.00000
   						      >	           -0.00000   -1.00000   -0.00000
   						      >	            0.00000    0.00000    1.00000
   						      >	    ITK_original_spacing = [1.00000, 1.00000, 1.00000]
   ITK_sform_corrected = NO					    ITK_sform_corrected = NO
   bitpix = 16							    bitpix = 16
   cal_max = 10000						    cal_max = 10000
   cal_min = 0							    cal_min = 0
   datatype = 4						    datatype = 4
   descrip = mnc2nii mni_icbm152_nlin_asym_09c/mni_icbm152_t	    descrip = mnc2nii mni_icbm152_nlin_asym_09c/mni_icbm152_t
   dim[0] = 3							    dim[0] = 3
   dim[1] = 193						    dim[1] = 193
   dim[2] = 229						    dim[2] = 229
   dim[3] = 193						    dim[3] = 193
   dim[4] = 1							    dim[4] = 1
   dim[5] = 1							    dim[5] = 1
   dim[6] = 0							    dim[6] = 0
   dim[7] = 0							    dim[7] = 0
   dim_info = 0						    dim_info = 0
   intent_code = 0						    intent_code = 0
   intent_p1 = 0						    intent_p1 = 0
   intent_p2 = 0						    intent_p2 = 0
   intent_p3 = 0						    intent_p3 = 0
   nifti_type = 1						    nifti_type = 1
   pixdim[0] = 0						    pixdim[0] = 0
   pixdim[1] = 1						    pixdim[1] = 1
   pixdim[2] = 1						    pixdim[2] = 1
   pixdim[3] = 1						    pixdim[3] = 1
   pixdim[4] = 0						    pixdim[4] = 0
   pixdim[5] = 1						    pixdim[5] = 1
   pixdim[6] = 0						    pixdim[6] = 0
   pixdim[7] = 0						    pixdim[7] = 0
   qfac = 1						      |	    qfac = 1.00000
   qform_code = 4						    qform_code = 4
   qform_code_name = NIFTI_XFORM_MNI_152			    qform_code_name = NIFTI_XFORM_MNI_152
   qoffset_x = -96						    qoffset_x = -96
   qoffset_y = -132						    qoffset_y = -132
   qoffset_z = -78						    qoffset_z = -78
   qto_xyz of unsupported type N3itk6MatrixIfLj4ELj4EEE      |	    qto_xyz =
   						      >	            1.00000    0.00000    0.00000  -96.00000
   						      >	            0.00000    1.00000    0.00000 -132.00000
   						      >	            0.00000    0.00000    1.00000  -78.00000
   						      >	            0.00000    0.00000    0.00000    1.00000
   quatern_b = 0						    quatern_b = 0
   quatern_c = 0						    quatern_c = 0
   quatern_d = 0						    quatern_d = 0
   scl_inter = 0						    scl_inter = 0
   scl_slope = 1						    scl_slope = 1
   sform_code = 4						    sform_code = 4
   sform_code_name = NIFTI_XFORM_MNI_152			    sform_code_name = NIFTI_XFORM_MNI_152
   slice_code = 0						    slice_code = 0
   slice_duration = 0						    slice_duration = 0
   slice_end = 0						    slice_end = 0
   slice_start = 0						    slice_start = 0
   srow_x = 1 0 0 -96						    srow_x = 1 0 0 -96
   srow_y = 0 1 0 -132						    srow_y = 0 1 0 -132
   srow_z = 0 0 1 -78						    srow_z = 0 0 1 -78
   toffset = 0							    toffset = 0
   vox_offset = 352						    vox_offset = 352
   xyzt_units = 10						    xyzt_units = 10

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cookpa commented Oct 2, 2025

IDK why qfac is a float now, will fix

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cookpa commented Oct 2, 2025

Actually, it would need to be fixed upstream. The ITK metadata stores qfac as a float, and the rest of the pixdims as strings.

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cookpa commented Oct 2, 2025

Clarifying that the "Voxel->RAS" transform is Voxel->RAS+.

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cookpa commented Oct 6, 2025

I'm thinking about removing the "Voxel->RAS+ x-form" output because I think it might become confusing, we use ITK LPS+ coordinates throughout ANTsX.

@cookpa cookpa merged commit 164c8f1 into master Oct 7, 2025
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@cookpa cookpa deleted the fix_matrix_header_print branch October 7, 2025 19:32
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Error messages about invalid direction in PrintHeader

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@cookpa @gdevenyi