Skip to content

plain C implementation of jmsh/bmsh output, -d 0/1 for output precision, accept .jnii input #1

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
wants to merge 14 commits into
base: main
Choose a base branch
from
Open

plain C implementation of jmsh/bmsh output, -d 0/1 for output precision, accept .jnii input #1

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
14 commits
Select commit Hold shift + click to select a range
4567dd4
output in bmsh format
fangq Apr 16, 2022
d1c6edd
support -d 0/1 to export double/single, support isGz in bmsh
fangq Apr 16, 2022
f00991a
reimplement save_jmsh without cJSON to reduce exe size
fangq Apr 17, 2022
b131c1a
accept JSON-based JNIfTI (.jnii) file as input volume, 'make JSON=1'
fangq Apr 17, 2022
8905521
change jnii data to column major to match nii
fangq Apr 18, 2022
3cdbdb1
fix gcc error when compiling with OLD=1
fangq Apr 18, 2022
288ac4a
Fix issue 2 (https://github.com/neurolabusc/nii2mesh/issues/2)
neurolabusc Apr 19, 2022
1b7403d
report an error when the specified .jnii file is missing
fangq Apr 19, 2022
4e60564
Merge pull request #1 from rordenlab/main
fangq Apr 19, 2022
a41c4bc
fix all gcc -Wall --pedantic warnings, #1
fangq Apr 19, 2022
fca6bb5
slight update to README
fangq Apr 19, 2022
2c28bbc
update URLs to use https
fangq Apr 19, 2022
c670126
remote instruction on make JSON=1 for jmsh output in README
fangq Apr 19, 2022
848cb1d
stop encoding slash in JSON strings, see https://mondotondo.com/2010/…
fangq Apr 20, 2022
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
14 changes: 8 additions & 6 deletions README.md
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
## About

This tool converts a NIfTI 3D voxel image to a triangulated mesh. It can save meshes in in the GIfTI (.gii), mz3, obj, ply, FreeSurfer (.pial), stl, vtk, formats. You can use [dcm2niix](https://github.com/rordenlab/dcm2niix) to convert DICOM images to NIfTI. The software is written in pure C (rather than C++).
This tool converts a NIfTI 3D voxel image to a triangulated mesh. It can save meshes in in the GIfTI (.gii), mz3, [JMesh](https://github.com/NeuroJSON/jmesh) (.jmsh, .bmsh), obj, ply, FreeSurfer (.pial), stl, vtk, formats. You can use [dcm2niix](https://github.com/rordenlab/dcm2niix) to convert DICOM images to NIfTI. The software is written in pure C (rather than C++).

## Compiling

Expand Down Expand Up @@ -52,10 +52,11 @@ Options
-o v Original marching cubes (0=Improved Lewiner, 1=Original, default 0)
-p v pre-smoothing (0=skip, 1=smooth, default 1)
-r v reduction factor (default 0.25)
-q v quality (0=fast, 1= balanced, 2=best, default 1)
-q v quality (0=fast, 1=balanced, 2=best, default 1)
-d v double precision (0=use single precision, 1=use double precision (for bmsh/json), default 0)
-s v post-smoothing iterations (default 0)
-v v verbose (0=silent, 1=verbose, default 0)
mesh extension sets format (.gii, .mz3, .obj, .ply, .pial, .stl, .vtk)
mesh extension sets format (.gii, .mz3, .bmsh, .jmsh, .json, .obj, .ply, .pial, .stl, .vtk)
Example: './nii2mesh voxels.nii mesh.obj'
Example: './nii2mesh bet.nii.gz -i 22 myOutput.obj'
Example: './nii2mesh bet.nii.gz -i b bright.obj'
Expand Down Expand Up @@ -165,16 +166,17 @@ with the resulting meshes have the file names `D99_pu.k1.gii`, `D99_cd.k2.gii`,

## Supported Mesh Formats

nii2mesh can save meshes to the GIfTI (.gii), json, jmsh, mz3, obj, off, ply, FreeSurfer (.pial), stl, vtk. [MeshLab](https://www.meshlab.net) can export meshes to many other formats. Therefore, one option is to create a PLY mesh with nii2mesh and use MeshLab to export to your favorite format.
nii2mesh can save meshes to the GIfTI (.gii), JSON, JMesh (.jmsh, .bmsh), mz3, obj, off, ply, FreeSurfer (.pial), stl, vtk. [MeshLab](https://www.meshlab.net) can export meshes to many other formats. Therefore, one option is to create a PLY mesh with nii2mesh and use MeshLab to export to your favorite format.

- [GIfTI](https://www.nitrc.org/projects/gifti/) is a popular Geometry format for Neuroimaging. The usage of base64 encoding leads to relatively large files and slow loading.
- [OBJ](http://www.paulbourke.net/dataformats/obj/) format is very popular, and may be a great choice for 3D printing. The use of ASCII rather than binary encoding makes these files large, slow to read and typically suggests limited precision.
- [OFF](https://en.wikipedia.org/wiki/OFF_(file_format)) is a classic ASCII format.
- [PLY](http://paulbourke.net/dataformats/ply/) is an old format that is widely supported. The binary form created by nii2mesh yields small files and quick loading time.
- [MZ3](https://github.com/neurolabusc/surf-ice/tree/master/mz3) is the native format of [Surfice](https://www.nitrc.org/projects/surfice/). It is small and fast, but not widely supported.
- [FreeSurfer](https://surfer.nmr.mgh.harvard.edu) format is simple and used by FreeSurfer.
- [json](https://github.com/fangq/jmesh) creates human readable ASCII JSON files in the format described by [jmesh](https://github.com/fangq/jmesh). Be aware that other tools create legal JSON files to describe triangular meshes using a structure that is not compatible with json.
- [jmsh](https://github.com/fangq/jmesh) files are in the [jmesh](https://github.com/fangq/jmesh) format, which inserts a compressed binary stream into a human readable JSON file. Supporting this format slightly increases the size of the executable (using the optional `-DHAVE_JSON` compiler flag and `cJSON` files).
- [JSON](https://github.com/NeuroJSON/jmesh) creates human readable ASCII JSON files in the format described by [JMesh specification](https://github.com/NeuroJSON/jmesh). Be aware that other tools create legal JSON files to describe triangular meshes using a structure that is not compatible with json.
- [JMSH](https://github.com/NeuroJSON/jmesh) files are in the [NeuroJSON](https://neurojson.org) [JMesh](https://github.com/fangq/jmesh) format, which inserts a compressed binary stream into a human readable JSON file.
- [BMSH](https://github.com/NeuroJSON/jmesh) is a binary-JSON ([BJData - Draft 2](https://github.com/NeuroJSON/bjdata/blob/Draft_2/Binary_JData_Specification.md)) based mesh-data container based on the JMesh specification; both `.bmsh` and `.jmsh` support data-level compression
- [VTK](http://www.princeton.edu/~efeibush/viscourse/vtk.pdf) refers to the legacy VTK format, which is supported by many tools (unlike the more flexible modern XML-based VTK formats).
- [STL](http://www.paulbourke.net/dataformats/stl/) format is popular for 3D printing. You should use any other format unless required. This format does not re-use vertices across triangles, this results in very large files. Further, this means the meshes are either slow to load or appear to have a faceted jagged appearance.

Expand Down
3 changes: 2 additions & 1 deletion data/README.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -4,4 +4,5 @@ This folder contains NIfTI format images for evaluating mesh conversion.
- `BET.nii.gz` [T1-weighted image](https://github.com/neurolabusc/dcm_qa_philips_enh) after [Brain Extraction](https://github.com/MIC-DKFZ/HD-BET). Two spheres have been added outside the left hemisphere: an anterior, binary, hollow sphere as well as a posterior, fuzzy, solid sphere.
- `pve_1.nii.gz` [FAST](https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FAST) gray matter segmentation.
- `pve_2.nii.gz` [FAST](https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FAST) white matter segmentation.
- `D99_atlas_v2.0_right.nii.gz` is the [Macaque Atlas v2.0](https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/nonhuman/macaque_tempatl/atlas_d99v2.html)
- `D99_atlas_v2.0_right.nii.gz` is the [Macaque Atlas v2.0](https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/nonhuman/macaque_tempatl/atlas_d99v2.html)
- `digimouse.jnii` [JNIfTI](http://neurojson.org/jnifti/draft1) formatted [Digimouse Atlas](https://neuroimage.usc.edu/neuro/Digimouse_Download), see Fig. 9 of [BlenderPhotonics paper](https://doi.org/10.1117/1.jbo.27.8.083014)
Loading