= Co-registration of dissection photographs of coronal slabs into a 3D volume (legacy version, 2024) =

'''''This command was replaced by a newer version in May 2025; please see: [[https://surfer.nmr.mgh.harvard.edu/fswiki/mri_3d_photo_recon]].'''''

If you use this tools in your analysis, please cite:
 
* [[https://elifesciences.org/articles/91398|Machine learning of dissection photographs and surface scanning for quantitative 3D neuropathology]]. H Gazula, H Tregidgo, B Billot, Y Balbastre, J Williams Ramirez, R Herisse, LJ Deden-Binder, A Casamitjana, EJ Melief, CS Latimer, MD Kilgore, M Montine, E Robinson, E Blackburn, MS Marshall, TR Connors, DH Oakley, MP Frosh, SI Young, K Van Leemput, AV Dalca, B Fischl, CL Mac Donald, CD Keene,  B Hyman, and JE Iglesias. Under revision.)


mri_3d_photo_recon -h
||--input_photo_dir ||Directory with input pixel-corrected photos. ||
||--input_segmentation_dir ||Directory with input slab masks/segmentations ||
||--ref_mask ||When using a binary volume as a reference. ||
||--ref_surface ||Using a 3D surface scan as a reference. ||
||--ref_soft_mask ||Using the provided average atlas. Best for using retrospective processing on data without a better reference. ||
||--mesh_reorient_with_indices ||Vertex indices of the frontal pole, occipital pole, and top of the central sulcus, separated with commas, for mesh alignment. ||
||--photos_of_posterior_side ||Use when photos are taken of the posterior side of slabs (default is anterior side). ||
||--order_posterior_to_anterior ||Use when photos are ordered from posterior to anterior (default is anterior to posterior). ||
||--allow_z_stretch ||Use to adjust the slice thickness to best match the reference. You should probably '''*never*''' use this with soft references (ref_soft_mask). ||
||--rigid_only_for_photos ||Switch on if you want photos to deform only rigidly (not affine). ||
||--slice_thickness ||Slice thickness in mm. ||
||--photo_resolution ||Resolution of the photos in mm. ||
||--output_directory ||Output directory with reconstructed photo volume and reference. ||



<<BR>>

In Freeview, you can find the number corresponding to the vertices of each anatomical area to use in the --mesh_reorient_with_indices flag. These indices should be comma-separated in the order: frontal pole, occipital pole, and top of the central sulcus.<<BR>>
|| {{attachment:43_vertexFP.png||width="304",height="254"}} || {{attachment:44_vertexOP.png||width="297",height="249"}} || {{attachment:45_vertexCS.png||width="302",height="253"}} ||
||Frontal Pole ||Occipital Pole ||Top of the central sulcus ||
For example, the --mesh_reorient_with_indices flag might look like this:
 . –mesh_reorient_with_indices 999999,999999,999999
'''Example for running reconstruction''' <<BR>>
 . mri_3d_photo_recon \
 . --input_photo_dir ./deformed \
 . --input_segmentation_dir ./connected_components \
 . --ref_surface ./mesh/case.stl \
 . --mesh_reorient_with_indices 999,1010,333333 \
 . --photos_of_posterior_side --allow_z_stretch \
 . --slice_thickness 8 \
 . --photo_resolution 0.1