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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.

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 ||
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.


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

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

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	= 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]].'''''