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| Describe mri_3d_photo_recon here. |
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 |
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.
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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