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.

43_vertexFP.png

44_vertexOP.png

45_vertexCS.png

Frontal Pole

Occipital Pole

Top of the central sulcus

For example, the --mesh_reorient_with_indices flag might look like this:

Example for running reconstruction