Improve description of nii2mesh features

README.md

@@ -8,7 +8,7 @@ To read the WASM specific README, please click [here](./js/README.md). The rest
 
 ## About
 
-It is said that `imitation is the sincerest form of flattery`. This project emulates the popular [fslmaths](https://fsl.fmrib.ox.ac.uk/fslcourse/lectures/practicals/intro3/index.html) tool. fslmaths is advertized as a `general image calculator` and is not only one of the foundational tools for FSL's brain imaging pipelines (such as [FEAT](https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FEAT)), but has also been widely adopted by many tools. This popularity suggests that it fulfills an important niche. While scientists are often encouraged to discover novel solutions, it sometimes seems that replication is undervalued. Here are some specific reasons for creating this tool:
+It is said that `imitation is the sincerest form of flattery`. This project emulates the popular [fslmaths](https://fsl.fmrib.ox.ac.uk/fslcourse/lectures/practicals/intro3/index.html) tool. fslmaths is a `general image calculator` and is not only one of the foundational tools for FSL's brain imaging pipelines (such as [FEAT](https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FEAT)), but has also been widely adopted by many tools. This popularity suggests that it fulfills an important niche. While scientists are often encouraged to discover novel solutions, it sometimes seems that replication is undervalued. Here are some specific reasons for creating this tool:
 
 1. While fslmaths is provided for without charge, it is not [open source](https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Licence). This limits its inclusion in other projects, in particular for commercial exploitation.
 2. Using an open source license allows niimath to build with open source libraries that the FSL team can not use. Specifically, the CloudFlare zlib provides dramatically faster performance than the public domain library used by fslmaths. n.b. Subsequently, we helped update [CloudFlare zlib](https://github.com/cloudflare/zlib/pull/19) that allows recent FSL releases to use this library,  improving the speed for all FSL tools.
@@ -188,7 +188,7 @@ Here are the same testson a desktop computer with twelve cores (24 threads, Ryze
 
 ## Converting voxelwise images to a triangulated mesh
 
-niimath can convert NIfTI images to meshes, suitable for viewing in Surfice, blender, SUMA, FreeSurfer and other tools. The features are based on [nii2mesh](https://github.com/neurolabusc/nii2mesh) and the features are almost identical. However, the order of arguments is different to match the expectations of fslmaths/niimath. So the call `nii2mesh -r 1 bet.nii.gz r100.ply` becomes `niimath bet.nii.gz -mesh -r 1 r100.ply`. As described on the nii2mesh page, you can create independent meshes for each area in an atlas using the command:
+niimath can convert NIfTI images to meshes, suitable for viewing in Surfice, blender, SUMA, FreeSurfer and other tools. The features are based on [nii2mesh](https://github.com/neurolabusc/nii2mesh) and the features are almost identical. However, the order of arguments is different to match the expectations of fslmaths/niimath. So the call `nii2mesh -r 1 bet.nii.gz r100.ply` becomes `niimath bet.nii.gz -mesh -r 1 r100.ply`. The benefit of niimath is that you can apply voxel-based operations before you create your mesh. This allows you to apply morphological operations (`-close`, `-ero`, `-dilM`). As an example, to apply a 4mm Gaussian smooth before creating a mesh, you could run `./niimath mni152.nii.gz -s 4 -mesh -i 122 -l 0 -b 1 b1.ply`. As described on the [nii2mesh](https://github.com/neurolabusc/nii2mesh) page, you can create independent meshes for each area in an atlas using the command:
 
 ```
 niimath D99_atlas_v2.0_right.nii.gz -mesh -p 0 -s 10 -a D99_v2.0_labels_semicolon.txt ./gii/D99s10roi.gii
@@ -208,7 +208,10 @@ niimath can also be compiled to WebAssembly (Wasm) allowing it to be inserted in
 
 ## License
 
-niimath is licensed under the 2-Clause BSD License. Except where noted, the code was written by Chris Rorden in 2020-2022. The code in `tensor.c` was written by Daniel Glen (2004) from the US National Institutes of Health and is not copyrighted (though it is included here with the permission of the author). The FSL team graciously allowed the text strings (help, warning and error messages) to be copied verbatim. The Butterworth Filter Coefficients in `bw.c` are from [Exstrom Labs](http://www.exstrom.com/journal/sigproc/) and the authors provided permission for it to be included in this project under the [LGPL](https://www.gnu.org/licenses/lgpl-3.0.en.html), the file provides additional details. Taylor Hanayik from the FSL group provided pseudo-code for some functions where there is little available documentation. The PolygoniseCube function comes from Cory Bloyd's public domain [Marching Cubes example](http://paulbourke.net/geometry/polygonise/) program described here. The bwlabel.cpp file was written by Jesper Andersson, who has explicitly allowed this to be shared using the BSD 2-Clause license. The [high performance](https://github.com/gaspardpetit/base64) base64.cpp was written by Jouni Malinen and is distributed under the BSD license. The mesh simplification was written by [Sven Forstmann](https://github.com/sp4cerat/Fast-Quadric-Mesh-Simplification) and distributed under the MIT license. It was ported from C++ to C by Chris Rorden.  The [radixsort.c](https://github.com/bitshifter/radixsort) was written by Cameron Hart (2014) using the zlib license.
+# codespell-ignore-next
+Hart
+
+<!-- codespell-ignore-line --> niimath is licensed under the 2-Clause BSD License. Except where noted, the code was written by Chris Rorden in 2020-2022. The code in `tensor.c` was written by Daniel Glen (2004) from the US National Institutes of Health and is not copyrighted (though it is included here with the permission of the author). The FSL team graciously allowed the text strings (help, warning and error messages) to be copied verbatim. The Butterworth Filter Coefficients in `bw.c` are from [Exstrom Labs](http://www.exstrom.com/journal/sigproc/) and the authors provided permission for it to be included in this project under the [LGPL](https://www.gnu.org/licenses/lgpl-3.0.en.html), the file provides additional details. Taylor Hanayik from the FSL group provided pseudo-code for some functions where there is little available documentation. The PolygoniseCube function comes from Cory Bloyd's public domain [Marching Cubes example](http://paulbourke.net/geometry/polygonise/) program described here. The bwlabel.cpp file was written by Jesper Andersson, who has explicitly allowed this to be shared using the BSD 2-Clause license. The [high performance](https://github.com/gaspardpetit/base64) base64.cpp was written by Jouni Malinen and is distributed under the BSD license. The mesh simplification was written by [Sven Forstmann](https://github.com/sp4cerat/Fast-Quadric-Mesh-Simplification) and distributed under the MIT license. It was ported from C++ to C by Chris Rorden.  The [radixsort.c](https://github.com/bitshifter/radixsort) was written by Cameron Hart (2014) using the zlib license.
 
 ## Links
 

src/bwlabel.c

@@ -414,6 +414,7 @@ int bwlabel(float *img, int conn, size_t dim[3], bool onlyLargest, bool fillBubb
     for (int i = 0; i < nvox; i++)
       l[i] = (l[i] == mxL);
     nl = 1;
+    free(nls);
   } //if labels found
   if (fillBubbles)
       fillh(l, dim, 0, nl);

src/niimath.c

@@ -61,7 +61,7 @@
 	#define kOS "Windows"
 #endif
 
-#define kMTHdate "v1.0.20240817"
+#define kMTHdate "v1.0.20240905"
 #define kMTHvers kMTHdate kOMPsuf kCCsuf
 
 #ifdef NII2MESH

src/oldcubes.c

@@ -495,6 +495,7 @@ int marchingCubes(float * img, short dim[3], int lo[3], int hi[3], int originalM
 	}
 	if (npt < 3) {
 		free(pts);
+		printf("marching cubes failed to identify triangles with an isolevel of %g\n", isolevel);
 		return EXIT_FAILURE;
 	}
 	*vs = (vec3d *) malloc(npt*sizeof(vec3d));