diff --git a/ext_libs/iso2mesh/binscork.mexa64 b/ext_libs/iso2mesh/bin/cork.mexa64
similarity index 100%
rename from ext_libs/iso2mesh/binscork.mexa64
rename to ext_libs/iso2mesh/bin/cork.mexa64
diff --git a/ext_libs/iso2mesh/binscork.mexmaci64 b/ext_libs/iso2mesh/bin/cork.mexmaci64
similarity index 100%
rename from ext_libs/iso2mesh/binscork.mexmaci64
rename to ext_libs/iso2mesh/bin/cork.mexmaci64
diff --git a/ext_libs/iso2mesh/doc/Advanced_Features.txt b/ext_libs/iso2mesh/doc/Advanced_Features.txt
deleted file mode 100755
index ff726d197..000000000
--- a/ext_libs/iso2mesh/doc/Advanced_Features.txt
+++ /dev/null
@@ -1,119 +0,0 @@
-   #[1]iso2mesh: a Matlab/Octave-based mesh generator
-
-Advanced Features in iso2mesh
-
-Global variables
-
-   ISO2MESH_TEMP
-          controls the temporary file output directory
-
-   The default output directory is under the system's temporary directory,
-   i.e. the output of mwpath(''). However, if one does not have permission
-   to write to this folder, or if this contains outputs from other users
-   who shares the same output folder (for example, /tmp/iso2mesh-username
-   on Linux), one can avoid the permission error by setting his own output
-   folder. To do this, he need to define
-   ISO2MESH_TEMP='/folder/path/you/can/write';
-
-   in Matlab/Octave's "base workspace". The iso2mesh commands afterward
-   will output the intermediate files under the specified temp directory.
-
-   ISO2MESH_SESSION
-          controls the output file name prefix
-
-   If two users share a common output directory (for example /tmp for GNU
-   Linux) on a single machine, some of the users may not able to write
-   intermediate output files and encountered errors. If this happens, one
-   can set "ISO2MESH_TEMP" to define a new output folder, alternatively,
-   one can set ISO2MESH_SESSION to label all his output by a unique
-   prefix. For example, if one define
-   ISO2MESH_SESSION='foo_';
-
-   this will prepend 'foo_' to all output file names, if this string is
-   unique, users can produce all their output files without conflict with
-   other users.
-
-   ISO2MESH_BIN
-          specifies the folder where to look for the external binaries
-
-   There are several external tools are essential for iso2mesh. These
-   pre-compiled binaries are saved under iso2mesh/bin folder. In our
-   [2]Installation instructions, we ask the users to add this path to
-   their PATH environment variable. If user for some reason not be able to
-   do this, iso2mesh will do two things to look for these binaries:
-    1. it will first check a global variable ISO2MESH_BIN and see if it is
-       defined in the 'base' workspace, if it is defined and the folder
-       exist, it will execute the binaries from that folder
-    2. if no ISO2MESH_BIN defined, or it has a value which does not exist,
-       iso2mesh will use the relative path "iso2mesh/bin" to load those
-       binaries
-    3. otherwise, it will give an error message, complaining the binary
-       can not be found.
-
-   ISO2MESH_RANDSEED
-          sets the seed for the random number generators in the CGAL
-          modules
-
-   Iso2mesh versions later than 1.0.0 can make reproducible meshes across
-   multiple runs. This was done by setting proper seeds for the random
-   number generators called inside the CGAL executables. By default,
-   iso2mesh will use 0x623F9A9E as the seed. If you prefer to set your own
-   seed, please define a global variable named ISO2MESH_RANDSEED in the
-   "base" workspace. The value of ISO2MESH_RANDSEED must be a positive
-   integer. If iso2mesh detects the definition of ISO2MESH_RANDSEED, it
-   will use it to seed the RNGs.
-
-Intermediate outputs
-
-   For each step of the mesh generation along the [3]work-flow, iso2mesh
-   will save some intermediate outputs as logs. These outputs are saved
-   under the output of mwpath('') (see the explanations for ISO2MESH_TEMP
-   above).
-
-   pre_extract.inr
-          if one use the default 'cgalsurf' method in vol2surf to extract
-          an isosurface from a binary image, this file will save the raw
-          binary image for each level set (only the last levelset stays)
-
-   post_extract.off
-          the output surface mesh from 'cgalsurf' method (vol2surf)
-
-   pre_remesh.off
-          if one use the 'simplify' option of vol2surf, this file saves
-          the voxel-resolution surface mesh extracted using binsurface
-          subroutine
-
-   post_remesh.off
-          this file records the triangular surface after mesh
-          simplifications (meshresample)
-
-   pre_sclean.off
-          for 'simplify' approach, this file is the surface mesh before
-          the mesh validation (meshcheckrepair)
-
-   post_sclean.off
-          this is the output from 'mechcheckrepair' subroutine.
-
-   post_vmesh.poly
-          when generating the 3D tetrahedral mesh, tetgen needs an input
-          file with PLC (piece-wise linear complexes) which is saved in
-          this poly file.
-
-   post_vmesh.off
-          if no bounding box needed, this file saves the same info as the
-          poly file, except it is in off format.
-
-   post_vmesh.1.ele
-          tetgen output: tetrahedral element file
-
-   post_vmesh.1.face
-          tetgen output: boundary surface element file
-
-   post_vmesh.1.node
-          tetgen output: node file
-
-References
-
-   1. http://iso2mesh.sourceforge.net/cgi-bin/index.cgi?action=rss
-   2. http://iso2mesh.sourceforge.net/cgi-bin/index.cgi?Doc/Installation
-   3. http://iso2mesh.sourceforge.net/cgi-bin/index.cgi?Doc/Workflow
diff --git a/ext_libs/iso2mesh/doc/Download_and_License.txt b/ext_libs/iso2mesh/doc/Download_and_License.txt
deleted file mode 100755
index 25f77e3b5..000000000
--- a/ext_libs/iso2mesh/doc/Download_and_License.txt
+++ /dev/null
@@ -1,138 +0,0 @@
-   #[1]iso2mesh: a Matlab/Octave-based mesh generator
-
-How to obtain iso2mesh
-
-          1. [2]Download the latest release
-
-          2. [3]Download Development Snapshot from SVN (not fully tested)
-
-                2.1. [4]Anonymous SVN Access
-
-                2.2. [5]Developer SVN Access
-
-          3. [6]Important Note on Licenses
-
-1. Download the latest release
-
-iso2mesh 2013 (1.5.0), codenamed [7]Laba Porridge
-
-   Please download the latest v1.5.0 release at our
-   [8]registration/download page. We are greatly appreciated if you can
-   tell us a little bit about you and your related research by
-   [9]registering your copy of iso2mesh.
-     * Release date: July 16, 2013
-     * This software is supported on [os-icons3.png]
-
-iso2mesh 1.4.9, codenamed Laba Porridge (beta)
-
-   Please download the stable v1.4.9 release at our
-   [10]registration/download page.
-     * Release date: Jan. 20, 2013
-
-2. Download Development Snapshot from SVN (not fully tested)
-
-   If you want to get the latest development branch of iso2mesh, you have
-   to download it from our subversion (SVN) repository. You have to be
-   aware that an SVN snapshot is not a stable release. It may contain
-   partially implemented features and, thus, cause crash or erroneous
-   results.
-
-   First, make sure you have installed an SVN client on your system. If
-   your system is a Debian-based GNU/Linux system (such as Ubuntu, Knoppix
-   etc), you can install SVN by
- sudo apt-get install subversion
-
-   if you are using a Redhat-based GNU/Linux system (such as Fedora,
-   CentOS etc), you can do this by
- su -c 'yum install subversion'
-
-   If your operating system is Windows, we recommend you installing
-   [11]TortoiseSVN.
-
-2.1. Anonymous SVN Access
-
-   The latest code snapshot can be checked out from project's [12]SVN
-   repository. It can be checked out anonymously by the following command.
-
- svn checkout svn://svn.code.sf.net/p/iso2mesh/code/trunk/iso2mesh iso2mesh
-
-   After checking out the code, you need to set up the path based on the
-   [13]installation instructions. Then you can start matlab or octave, and
-   run the example scripts under the sample directory.
-
-2.2. Developer SVN Access
-
-   If you are one of the developers who have SVN write-permission, you can
-   checkout the latest code with the same command above.
-
-   You will have to [14]register an account and ask the [15]project
-   maintainer to grant you SVN permission).
-
-   Once checkout, you can simply make changes or debug your changes in
-   your local copy. If your local changes have passed review by other
-   co-developers, you can then commit your changes back to the SVN
-   repository by
-
- cd /path/to/iso2mesh/local/copy
- svn commit -m "a short summary of your changes"
-
-3. Important Note on Licenses
-
-   The iso2mesh toolbox is licensed under [16]GNU Public License (GPL).
-   However, it included a number of external tools (under bin/ directory)
-   to perform certain functionality by means of [17]pipelines. These
-   external tools are subjected to their upstream licenses and are not
-   necessarily GPL (or GPL compatible). The complete list of these
-   external commands and their author info and licenses can be found from
-   the [18]README page.
-
-   Particularly, the 3D meshing tool, tetgen, is licensed under a non-free
-   license: it can be freely used, modified, redistributed only for
-   research and academic purposes, any commercial utility of tetgen
-   requires a permission from its [19]original author. iso2mesh calls
-   tetgen in the background to produce 3D mesh, that means if anyone needs
-   to uses the 3D mesh produced by iso2mesh in a commercial product, you
-   MUST contact the author of tetgen to get permission. Processing binary
-   images and produce surfaces are not subject to this limitation.
-
-   In additional to the licenses, if you use this tool in your research,
-   we are greatly appreciated if you can add iso2mesh to your references:
-
- Qianqian Fang, iso2mesh: a matlab-based 3D tetrahedral mesh generator, URL: [20]http://iso2mesh.sourceforge.net, 2008
-
-   or
-
- Qianqian Fang and David Boas, "Tetrahedral mesh generation from volumetric binary and gray-scale images,"
- Proceedings of IEEE International Symposium on Biomedical Imaging 2009, pp. 1142-1145, 2009
-
-   If you used cgalsurf or cgalmesh options in your mesh preparation, you
-   should also acknowledge [21]CGAL publications. If you generated your
-   mesh with the tetgen module in iso2mesh instead of CGAL mesher, you may
-   need to [22]acknowledge tetgen in your publications, you can find more
-   references from [23]this link.
-
-References
-
-   1. http://iso2mesh.sourceforge.net/cgi-bin/index.cgi?action=rss
-   2. http://iso2mesh.sourceforge.net/cgi-bin/index.cgi?Download#Download_the_latest_release
-   3. http://iso2mesh.sourceforge.net/cgi-bin/index.cgi?Download#Download_Development_Snapshot_from_SVN_not_fully_tested
-   4. http://iso2mesh.sourceforge.net/cgi-bin/index.cgi?Download#Anonymous_SVN_Access
-   5. http://iso2mesh.sourceforge.net/cgi-bin/index.cgi?Download#Developer_SVN_Access
-   6. http://iso2mesh.sourceforge.net/cgi-bin/index.cgi?Download#Important_Note_on_Licenses
-   7. http://en.wikipedia.org/wiki/Laba_Congee
-   8. http://iso2mesh.sourceforge.net/cgi-bin/index.cgi?register/iso2mesh
-   9. http://iso2mesh.sourceforge.net/cgi-bin/index.cgi?action=edit&id=register/iso2mesh
-  10. http://iso2mesh.sourceforge.net/cgi-bin/index.cgi?register/iso2mesh
-  11. http://tortoisesvn.net/downloads
-  12. http://sourceforge.net/p/iso2mesh/code/404/tree/
-  13. http://iso2mesh.sourceforge.net/cgi-bin/index.cgi?Doc/Installation
-  14. https://sourceforge.net/user/registration
-  15. http://sourceforge.net/users/fangq
-  16. http://www.gnu.org/licenses/gpl-2.0.html
-  17. http://en.wikipedia.org/wiki/Unix_pipe
-  18. http://iso2mesh.sourceforge.net/cgi-bin/index.cgi?Doc/README#Acknowledgement
-  19. http://www.wias-berlin.de/~si
-  20. http://iso2mesh.sourceforge.net/
-  21. http://www.cgal.org/bibliography.html
-  22. http://tetgen.berlios.de/reference.html
-  23. http://iso2mesh.sourceforge.net/cgi-bin/index.cgi?Doc/References
diff --git a/ext_libs/iso2mesh/doc/FAQ.txt b/ext_libs/iso2mesh/doc/FAQ.txt
deleted file mode 100755
index a78171a16..000000000
--- a/ext_libs/iso2mesh/doc/FAQ.txt
+++ /dev/null
@@ -1,273 +0,0 @@
-   #[1]iso2mesh: a Matlab/Octave-based mesh generator
-
-Frequently asked questions about iso2mesh
-
-          1. [2]I am getting a "Two subfaces ... are found intersecting
-          each other" error, what should I do?
-
-          2. [3]After mesh generation, the surface plot looks messed up,
-          what was wrong?
-
-          3. [4]Matlab complains about imread, imclose or imfill missing
-
-          4. [5]iso2mesh failed when writing files to disk
-
-          5. [6]When displaying a surface produced by iso2mesh, there are
-          many holes, how to fix this?
-
-          6. [7]Subroutine meshresample returns an empty mesh, why?
-
-          7. [8]Which meshing option should I choose?
-
-          8. [9]How do I control mesh density in iso2mesh?
-
-          9. [10]How to mesh a domain containing multiple isolated objects
-          ?
-
-1. I am getting a "Two subfaces ... are found intersecting each other" error, what should I do?
-
-   This is the most frequently encountered problem using this toolbox.
-   There are three possible causes of this error:
-
-1. the volume you are trying to mesh contains joint regions between more than 2 materials
-
-   This is most likely happening when you see the above error message. Try
-   to plot your volume slice by slice, and pay attention to any voxels
-   whose neighbors have more than 2 different values. If this is the case,
-   you can only use this type of input with vol2mesh/v2m with 'cgalmesh'
-   option as the "method" parameter. If you use either "simplify" or
-   "cgalsurf" (default) options, iso2mesh will fail. If for some reason
-   you have to use these options, here are two possible temporary
-   work-arounds:
-    1. if there are not many junction voxels, you may want to manually
-       edit your image and disconnect the regions that share the same
-       boundary and make sure all the sub-regions are either completely
-       disjointed, or completely enclosed by another.
-    2. merge the regions that have shared boundaries, and mesh the
-       resulting merged volume; after you get the tetrahedra, compute the
-       centroid of each element in the merged domain (identified by their
-       labels), and map them back to your original segmented image;
-       determine the original region id using the voxel containing the
-       centroids.
-
-   If you have any better suggestions to enable iso2mesh to handle this
-   situation, please let [11]me know.
-
-2. you are using 'simplify' method to mesh a complex domain
-
-   There are two possible methods for volume-to-surface conversion,
-   'simplify' and 'cgalsurf'. The second method always returns a
-   well-posed surface where no self-intersecting elements present;
-   however, the 'simplify' approach does not. The default method for
-   vol2mesh/vol2surf (v2m/v2s) is 'cgalsurf'. If you have to use
-   'simplify', you may have to experiment different surface densities for
-   the surface extraction. You may lucky enough to find a working
-   configuration, but very likely, you may not. Please use 'cgalsurf'
-   option whenever possible.
-
-3. your surface mesh is too coarse and intersects the enclosed surfaces
-
-   The mesh extraction will represent the region boundaries by a sheet of
-   triangles. Near sharp edges, this representation may generate a rounded
-   edge and does not exactly preserve the shape of the original domain. If
-   you happen to mesh a thin layer of material, the resulting surface may
-   intersect each other at sharp edges if your surface element is too big.
-   Please use a small opt.radbound value to run the mesh generation again.
-
-2. After mesh generation, the surface plot looks messed up, what was wrong?
-
-   It is very likely you incorrectly used the output variables. The output
-   of vol2mesh or surf2mesh include elem: the tetrahedral element indices,
-   and face: the surface triangle indices. But be careful, both of these
-   two arrays have an additional column. The last column is a label field,
-   indicating the origin (sub-region) of the elements. You should never
-   use the last columns of these two arrays for plotting. To make a
-   correct surface plot, you should use something like
- trisurf(face(:,1:3),node(:,1),node(:,2),node(:,3));
-
-   and don't use the full face array as the first parameter.
-
-   If you are using iso2mesh newer than 0.9.8, you can use a function
-   called "plotmesh" to visualize the produced surfaces and volumes. The
-   script will attempt to recognize the extra column of "face" by using
-   the Euler characteristics and automatically ignore it if present.
-
-3. Matlab complains about imread, imclose or imfill missing
-
-   Under the sample/ directory, demo_vol2mesh_ex2.m requires imread, which
-   is a build-in function in matlab, but not in octave. You have to
-   install octave-image via apt-get or yum first. In example
-   demo_vol2mesh_ex3.m, functions imclose and imfill are needed. These two
-   functions can only be found in matlab's image processing toolbox. If
-   you don't have this toolbox installed (of course, it is not free), you
-   can simply pass this example. For octave, unfortunately, these
-   functions do not exist yet, and hopefully someone can fill them in
-   soon.
-
-4. iso2mesh failed when writing files to disk
-
-   If you are working on a multi-user workstation, and multiple users were
-   using iso2mesh, some temporary files may have a conflict in read/write
-   permission under /tmp directory. If user A runs iso2mesh first, and
-   user B will get this error, because iso2mesh fails to create the
-   temporary files as it does not have the permissions to overwrite those
-   files created by A. To solve this issue, please define your own
-   temporary folder, or set your session id, you can find more info at
-   [12]Advanced page.
-
-5. When displaying a surface produced by iso2mesh, there are many holes, how to fix this?
-
-   The node orders in the output surface mesh are random, some are
-   oriented clockwise, some are counter-clockwise. This will make OpenGL,
-   or OpenGL based applications, render the surface with different
-   materials. To correct this, you can simply call
- [newnode,newface]=meshcheckrepair(node,face);
-
-   and the new surface: [newnode,newface] will have consistent
-   orientations. Again, be careful if you are using the face output from
-   vol2surf/v2s, it has an extra column. You only need to use the first 3
-   columns in the face array when making plots.
-
-6. Subroutine meshresample returns an empty mesh, why?
-
-   When the input surface mesh contains topological defects, such as
-   non-manifold nodes, the meshresample() subroutine will not proceed and
-   return an empty mesh (the output message will show "0 total edges
-   collapsed"). In this case, you need to first call meshcheckrepair()
-   subroutine to fix your input mesh, and them pass it to meshresample. An
-   example is shown below:
-  [no2,fc2]=meshcheckrepair(node_in,face_in);
-  [node_out,face_out]=meshresample(no2,fc2,0.2);
-
-   (this issue is automatically corrected in iso2mesh 0.8 or newer)
-
-7. Which meshing option should I choose?
-
-   Iso2mesh provides 3 options for v2m and vol2mesh, namely, 'cgalmesh',
-   'cgalsurf' and 'simplify'. Some users may get confused which one to
-   use. In fact, we were hoping not to put users in this situation, as
-   iso2mesh was designed for simplicity and efficiency. Unfortunately, we
-   haven't really found a single option that works for all of the
-   situations, and each of the 3 options have there good and bad sides.
-
-     * cgalmesh: this is the most powerful option of all, and is
-       potentially the ideal candidate as the default option. With
-       'cgalmesh', iso2mesh can easily process a binary volume and a
-       volume with multi-region labels with good speed and robustness. It
-       can produce both volumetric and surfaces meshes at the same time,
-       and clearly labels the element and surfaces for each individual
-       sub-region. However, it is not perfect. It can not extract
-       iso-surfaces from a gray-scale image. When you want to control mesh
-       densities near a specific isosurface (such as [13]this case),
-       cgalmesh option is not as flexible as the other two. In short,
-       cgalmesh is the best choice for producing uniform-sized meshes from
-       an arbitrary segmented volume.
-     * cgalsurf: cgalsurf option produces surface and volumetric meshes
-       with a standard 2-step process as shown in the [14]workflow. When
-       extracting multiple isosurfaces, it will do the extraction
-       sequentially. The strengths of cgalsurf include 1) all the
-       extracted surfaces are guaranteed to be free of self-intersecting
-       elements, individually, and 2) it can handle gray-scale volumes.
-       The main issue for cgalsurf is when multiple isosurfaces overlap to
-       each other, v2m/vol2mesh will break as the combined surface
-       contains self-intersecting elements. In short, cgalsurf is the best
-       option when multiple sub-regions are disconnected, or one enclosing
-       another.
-     * simplify: this is as flexible as cgalsurf, but it is not as
-       reliable. After the mesh simplification, a surface may become
-       self-intersecting and v2m/vol2mesh will stop working. However, when
-       you only have a dense surface to start with, this is the only
-       option you can use.
-
-   To make it easy to remember:
-    1. when meshing a simple binary volume, 'cgalmesh' and 'cgalsurf' are
-       both good choices
-    2. when meshing a segmented volumes with multiple sub-regions, use
-       'cgalmesh'
-    3. when meshing a gray-scale volume, use 'cgalsurf'
-    4. when other options fail, try 'simplify'.
-
-8. How do I control mesh density in iso2mesh?
-
-   Iso2mesh uses two parameters to quantitatively control the mesh
-   density. In v2m or vol2mesh, parameter opt sets the maximum edge length
-   of the surface triangles (i.e. controlling the density of the mesh on
-   the surface), and maxvol sets the maximum tetrahedron volume.
-
-   If you want to let the mesh be denser on the surface and coarser
-   inside, you can use a small opt value and a large maxvol value.
-
-   If you want to control the surface mesh density so that it adapts
-   depending on the curvature, you can do so by defining opt as a struct,
-   and set the opt.radbound and opt.distbound values. You can find
-   examples from [15]this presentation (slide 15). This example can also
-   be accessed from iso2mesh/sample/demo_helloworld.m
-
-9. How to mesh a domain containing multiple isolated objects ?
-
-   This is a known issue with the CGAL [16]surface mesher and [17]3D
-   mesher. A bug report has been filed [18]here, but it was not known if
-   any fix has been applied upstream.
-
-   For v2m/v2s with a 'cgalmesh' option, a simple work-around is to remove
-   zero-voxels by adding 1 to the 3D image. Then cgalmesher should be able
-   to recover all inclusions, along with the background. You can then
-   remove the background by checking the domain ID. For example:
-
-  [no,el]=v2m(uint8(img+1), [], opt, maxvol, 'cgalmesh');
-  el=el(find(el(:,5)>1),:);
-  [no,newel]=removeisolatednode(no(:,1:3),el(:,1:4));
-  newel(:,5)=el(:,5)-1;
-
-   If the target domain is a binary image, there is another work-around:
-function [node,elem]=meshisolatedobj(img,opt,maxvol)
-%
-% Usage:
-%    [node,elem]=meshisolatedobj(img,opt,maxvol)
-%    Author: Qianqian Fang <fangq at nmr.mgh.harvard.edu>
-%
-img=logical(img);
-[bin,regionnum]=bwlabeln(img,6);
-node=[];
-elem=[];
-
-for regionid=1:regionnum
-    fprintf(1,'meshing region #%d ...\n',regionid);
-
-    [no,el]=v2m(bin==regionid,0.5,opt,maxvol);
-
-    % merge the resulting mesh with other regions
-    el(:,5)=regionid;
-    el(:,1:4)=el(:,1:4)+size(node,1);
-    if(regionid>1)
-        elem=[elem;el];
-        node=[node;no];
-    else
-        node=no;
-        elem=el;
-    end
-end
-
-   This function only works in Matlab because function bwlabeln is not
-   available in Octave.
-
-References
-
-   1. http://iso2mesh.sourceforge.net/cgi-bin/index.cgi?action=rss
-   2. http://iso2mesh.sourceforge.net/cgi-bin/index.cgi?Doc/FAQ#I_am_getting_a_Two_subfaces_are_found_intersecting_each_other_error_what_should_I_do
-   3. http://iso2mesh.sourceforge.net/cgi-bin/index.cgi?Doc/FAQ#After_mesh_generation_the_surface_plot_looks_messed_up_what_was_wrong
-   4. http://iso2mesh.sourceforge.net/cgi-bin/index.cgi?Doc/FAQ#Matlab_complains_about_imread_imclose_or_imfill_missing
-   5. http://iso2mesh.sourceforge.net/cgi-bin/index.cgi?Doc/FAQ#iso2mesh_failed_when_writing_files_to_disk
-   6. http://iso2mesh.sourceforge.net/cgi-bin/index.cgi?Doc/FAQ#When_displaying_a_surface_produced_by_iso2mesh_there_are_many_holes_how_to_fix_this
-   7. http://iso2mesh.sourceforge.net/cgi-bin/index.cgi?Doc/FAQ#Subroutine_meshresample_returns_an_empty_mesh_why
-   8. http://iso2mesh.sourceforge.net/cgi-bin/index.cgi?Doc/FAQ#Which_meshing_option_should_I_choose
-   9. http://iso2mesh.sourceforge.net/cgi-bin/index.cgi?Doc/FAQ#How_do_I_control_mesh_density_in_iso2mesh
-  10. http://iso2mesh.sourceforge.net/cgi-bin/index.cgi?Doc/FAQ#How_to_mesh_a_domain_containing_multiple_isolated_objects
-  11. http://iso2mesh.sourceforge.net/cgi-bin/index.cgi?FangQ
-  12. http://iso2mesh.sourceforge.net/cgi-bin/index.cgi?Advanced
-  13. http://iso2mesh.sourceforge.net/upload/head_mesh.jpg
-  14. http://iso2mesh.sourceforge.net/cgi-bin/index.cgi?Doc/Workflow
-  15. http://iso2mesh.sf.net/upload/iso2mesh_a_one_liner_mesh_generator.pdf
-  16. http://www.cgal.org/Manual/latest/doc_html/cgal_manual/Surface_mesher/Chapter_main.html
-  17. http://www.cgal.org/Manual/latest/doc_html/cgal_manual/Mesh_3/Chapter_main.html
-  18. http://cgal-discuss.949826.n4.nabble.com/missing-objects-when-meshing-a-3D-image-with-multiple-disconnected-inclusions-td3349283.html
diff --git a/ext_libs/iso2mesh/doc/Get_Started.txt b/ext_libs/iso2mesh/doc/Get_Started.txt
deleted file mode 100755
index 6d7b152c7..000000000
--- a/ext_libs/iso2mesh/doc/Get_Started.txt
+++ /dev/null
@@ -1,55 +0,0 @@
-   #[1]iso2mesh: a Matlab/Octave-based mesh generator
-
-Getting Started with iso2mesh
-
-   Although iso2mesh provides a rich collection of [2]mesh-related
-   functions, the core functionality, i.e. creating volumetric meshes from
-   surfaces or binary image stacks, is very straightforward to use. A
-   minimum step to perform such task only requires about 3 to 5 lines of
-   matlab code. You can find a list of examples under the "sample"
-   directory. In [3]this page, we summarize the overall work-flow of this
-   toolbox.
-
-   To outline a simple meshing session, let's assume you have a 3D image
-   array, named "mydata", saved in a file called "mydata.mat". Variable
-   mydata can be any 3D image, an MRI/CT scan or a simple binary mask
-   produced by your own command. Here are the commands you need to produce
-   a volumetric FEM mesh from this volume:
-
- load mydata.mat
- [node,elem,face]=v2m(mydata,0.5,5,100);
- plotmesh(node,face)
-
-   Apparently, the first line loads the volumetric image data into your
-   current session. The second line calls an iso2mesh function, 'v2m', the
-   shortcut for vol2mesh, to construct a volumetric mesh from this data
-   array. The first argument of v2m, "mydata", is the volumetric image you
-   are about to mesh; the 2nd argument is the threshold value at which you
-   define the boundary surface of the mesh; the 3rd argument, 5, defines
-   the maximum size of the surface triangles; the last argument, 100,
-   defines the maximum volume of the resulting tetrahedral elements. You
-   can define a vector for the second argument, asking iso2mesh to produce
-   multiple level-sets as the exterior or internal interfaces of the
-   target domain. Both the 3rd and 4th arguments controls the density of
-   the resulting mesh: the smaller the values, the more triangles on the
-   surface and more tetrahedra in the volumetric mesh.
-
-   There are 3 outputs from v2m command:
-     * node: the node coordinates for the generated volumetric mesh, with
-       dimension of NN x 3, with each column being x, y and z,
-       respectively; NN is the number of nodes.
-     * elem: the tetrahedral element info, with a dimension of NE x 4, NE
-       being the number of tetrahedral elements; each row represents an
-       element, and each column are the node indices for each corner of a
-       tetrahedron.
-     * face: triangular surface element info, with a dimension of NS x 4,
-       NS being the number of surface triangles;the first 3 columns are
-       the node indices of each corner of the triangle, and the last
-       column is a flag to identify its mapping to the original surface
-       id.
-
-References
-
-   1. http://iso2mesh.sourceforge.net/cgi-bin/index.cgi?action=rss
-   2. http://iso2mesh.sourceforge.net/cgi-bin/index.cgi?Doc/FunctionList
-   3. http://iso2mesh.sourceforge.net/cgi-bin/index.cgi?Doc/Workflow
diff --git a/ext_libs/iso2mesh/doc/INSTALL.txt b/ext_libs/iso2mesh/doc/INSTALL.txt
deleted file mode 100755
index ca09895c7..000000000
--- a/ext_libs/iso2mesh/doc/INSTALL.txt
+++ /dev/null
@@ -1,76 +0,0 @@
-   #[1]iso2mesh: a Matlab/Octave-based mesh generator
-
-Installation Instructions for iso2mesh toolbox
-
-System Requirements
-
-   Iso2mesh is written in the Matlab language and is fully compatible with
-   [2]GNU Octave, as a result, any system that is capable of running
-   Matlab or Octave is able to run this toolbox in theory. However, as we
-   described in the [3]Doc/README, this toolbox relies on multiple
-   external tools/libraries for full functionality. So far, we have only
-   compiled these external tools for Linux (32/64bit), Mac OS (Intel based
-   or PowerPC based) and Windows (95~Windows 7, 32/64bit). If your
-   platform is not listed above (such as Solaris, AIX etc), please
-   download the [4]source code of these tools and compile them on your own
-   machine.
-
-   The recommended system configuration for running this toolbox includes
-     * a computer running GNU/Linux, Windows, Mac OS (either 32bit/64bit)
-     * standard installation of Matlab (v7 or above) or Octave (3.0 or
-       above) (for some demos, you need to install the image processing
-       toolbox for Matlab/Octave)
-     * 30M disk space for the toolbox and the examples
-     * a folder where you have write permission
-
-Installation
-
-   The installation of iso2mesh to your system is straightforward,
-   simplify following the instructions below:
-     * extract the downloaded package to a folder, for example,
-       /home/myaccount/work/iso2mesh, let's call it the "root directory"
-       of iso2mesh;
-     * start your Maltab, type addpath('/home/myaccount/work/iso2mesh') to
-       add iso2mesh to your Matlab search path for the current session
-          + if you want to add this path permanently for Matlab, you need
-            to type pathtool, browse to the iso2mesh root directory and
-            add it to the list, then click "Save"
-     * then, you can do a rehash in Matlab, and type which vol2mesh, if
-       you see an output, that means iso2mesh is now installed in Matlab
-     * you can navigate to a folder named "sample" inside iso2mesh's root
-       directory, and run the demo scripts, you should be able to see the
-       code complete with no error message. If it complains that some
-       commands can not be found, please make sure you have followed the
-       instructions above.
-
-For restricted users
-
-   You do not have to be a system administrator to install or use iso2mesh
-   toolbox. Most of the installation instructions can be done on a
-   per-user basis. The only issue a restricted user may encounter is the
-   "permission error" when saving the "pathtool" path list in order to add
-   iso2mesh permanently. If this happens, you may work in a multi-user or
-   network-based system. For Matlab users, you typically need to create
-   file named [5]startup.m under the [6]Matlab startup directory
-   (~/matlab/ for Linux/Unix), and put addpath('/path/to/iso2mesh/'); into
-   this file. It will be automatically executed when Matlab starts. For
-   Octave, this file is [7].octaverc.
-
-   When using this toolbox under an extensively restricted mode, one may
-   encounter a "fail to write" error, this may likely be caused by the
-   default output folder is not writable from your account. If you do have
-   another folder which you have permission to write, you need to
-   [8]define an variable ISO2MESH_TEMP in Matlab/Octave's "base workspace"
-   and set the value as the writable folder path, then rerun your meshing
-   commands.
-
-References
-
-   1. http://iso2mesh.sourceforge.net/cgi-bin/index.cgi?action=rss
-   2. http://www.gnu.org/software/octave/
-   3. http://iso2mesh.sourceforge.net/cgi-bin/index.cgi?Doc/README
-   4. http://sourceforge.net/p/iso2mesh/code/402/tree/trunk/
-   5. http://www.mathworks.com/access/helpdesk/help/techdoc/matlab_env/f8-4994.html#brlkmbe-1
-   6. http://www.mathworks.com/help/techdoc/matlab_env/f8-10506.html
-   7. http://en.wikibooks.org/wiki/MATLAB_Programming/Differences_between_Octave_and_MATLAB#startup.m
-   8. http://iso2mesh.sourceforge.net/cgi-bin/index.cgi?Advanced
diff --git a/ext_libs/iso2mesh/doc/gendoc.sh b/ext_libs/iso2mesh/doc/gendoc.sh
deleted file mode 100755
index e4b5d9790..000000000
--- a/ext_libs/iso2mesh/doc/gendoc.sh
+++ /dev/null
@@ -1,11 +0,0 @@
-#!/bin/sh
-
-# commands to update the document pages from homepage
-
-lynx -dont_wrap_pre -dump "http://iso2mesh.sourceforge.net/cgi-bin/index.cgi?keywords=Download&embed=1" > Download_and_License.txt
-lynx -dont_wrap_pre -dump "http://iso2mesh.sourceforge.net/cgi-bin/index.cgi?keywords=Doc/Installation&embed=1" > INSTALL.txt
-lynx -dont_wrap_pre -dump "http://iso2mesh.sourceforge.net/cgi-bin/index.cgi?keywords=Doc/Basics&embed=1" > Get_Started.txt
-lynx -dont_wrap_pre -dump "http://iso2mesh.sourceforge.net/cgi-bin/index.cgi?keywords=Doc/FAQ&embed=1" > FAQ.txt
-lynx -dont_wrap_pre -dump "http://iso2mesh.sourceforge.net/cgi-bin/index.cgi?keywords=Advanced&embed=1" > Advanced_Features.txt
-
-wget http://iso2mesh.sourceforge.net/upload/iso2mesh_workflow_v2.png -Oiso2mesh_workflow.png
diff --git a/ext_libs/iso2mesh/doc/iso2mesh_workflow.jpg b/ext_libs/iso2mesh/doc/iso2mesh_workflow.jpg
deleted file mode 100755
index 5e3b3d494..000000000
Binary files a/ext_libs/iso2mesh/doc/iso2mesh_workflow.jpg and /dev/null differ
diff --git a/ext_libs/iso2mesh/sample/brain.tif b/ext_libs/iso2mesh/sample/brain.tif
deleted file mode 100755
index de8d88bf3..000000000
Binary files a/ext_libs/iso2mesh/sample/brain.tif and /dev/null differ
diff --git a/ext_libs/iso2mesh/sample/brain_seg.tif b/ext_libs/iso2mesh/sample/brain_seg.tif
deleted file mode 100755
index ffdd6aac9..000000000
Binary files a/ext_libs/iso2mesh/sample/brain_seg.tif and /dev/null differ
diff --git a/ext_libs/iso2mesh/sample/demo_cgalmesher.m b/ext_libs/iso2mesh/sample/demo_cgalmesher.m
deleted file mode 100755
index b4152b976..000000000
--- a/ext_libs/iso2mesh/sample/demo_cgalmesher.m
+++ /dev/null
@@ -1,52 +0,0 @@
-% This example calls cgalmesher to mesh a segmented
-% brain volume. The segmentation was done by FreeSurfer
-% and there are 41 different types of tissues. Each tissue
-% type is labeled by a unique integer.
-
-fprintf(1,'loading segmented brain image...\n');
-for i=1:256
-  brain(:,:,i)=imread('brain_seg.tif',i);
-end
-brain=uint8(brain);
-
-% call cgalmesher to mesh the segmented volume
-% this will take 30 seconds on an Intel P4 2.4GHz PC
-
-fprintf(1,'meshing the segmented brain (this may take a few minutes) ...\n');
-
-[node,elem,face]=v2m(brain,[],2,100,'cgalmesh');
-
-figure
-hs=plotmesh(node,face,'y>100');
-
-axis equal;
-title('cross-cut view of the generated surface mesh');
-
-% find the sub-region number 3, it happens to be the right-hemisphere
-% cerebellum white matter. Use volface to extract the white matter surface.
-
-fprintf(1,'extracting the right-hemisphere cerebellum white matter surface\n')
-
-LHwhitemat=elem(find(elem(:,5)==5),:);
-wmsurf=volface(LHwhitemat(:,1:4));
-
-figure;
-hs=plotmesh(node,wmsurf);
-axis equal;
-title('pre-smoothed cerebellum white matter surface');
-
-
-fprintf(1,'performing mesh smoothing on the white matter surface\n')
-
-[no,el]=removeisolatednode(node,wmsurf);
-wmno=sms(no(:,1:3),el,3,0.5);
-
-figure;
-hs=plotmesh(wmno,el);
-axis equal;
-title('smoothed cerebellum white matter surface of the right-hemisphere');
-
-
-fprintf(1,'generate volumetric mesh from the smoothed cerebellum white matter surface \n')
-
-[wmnode,wmelem,wmface]=s2m(wmno(:,1:3),el(:,1:3),1,200);
diff --git a/ext_libs/iso2mesh/sample/demo_directplc_ex1.m b/ext_libs/iso2mesh/sample/demo_directplc_ex1.m
deleted file mode 100755
index 8a48bb293..000000000
--- a/ext_libs/iso2mesh/sample/demo_directplc_ex1.m
+++ /dev/null
@@ -1,51 +0,0 @@
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%% angular resolution
-dt=pi/40;		
-t=0:dt:2*pi-dt;
-
-%% parameters of a side-cut fiber
-h=100;
-r1=20;
-r2=25;
-a=-1;	 
-b=0;
-c=1;
-d=-h;
-
-%% key nodes of a side-cut fiber
-
-n1=[r1*sin(t(:)) r1*cos(t(:)) zeros(size(t(:)))];
-n2=[r2*sin(t(:)) r2*cos(t(:)) zeros(size(t(:)))];
-
-n3=[r1*sin(t(:)) r1*cos(t(:)) -d-(a*r1*sin(t(:))+b*r1*cos(t(:)))/c];
-n4=[r2*sin(t(:)) r2*cos(t(:)) -d-(a*r2*sin(t(:))+b*r2*cos(t(:)))/c];
-
-no=[n1;n2;n3;n4];
-
-%% PLCs of the side-cut fiber
-
-clear fc;
-count=1;  
-for i=1:length(t)-1
-   % the last number in each cell is the fc id
-   fc{count}={[i+length(t) i+3*length(t) i+3*length(t)+1 i+length(t)+1],1}; count=count+1;
-   fc{count}={[i i+2*length(t) i+2*length(t)+1 i+1],2}; count=count+1;
-end
-i=length(t);
-fc{count}={[i+length(t) i+3*length(t) 1+3*length(t) 1+length(t)],1}; count=count+1;
-fc{count}={[i i+2*length(t) 1+2*length(t) 1],2}; count=count+1;
-
-fc{count}={1:1+length(t)-1,3};count=count+1;  % bottom inner circle
-fc{count}={[1+length(t):1+length(t)*2-1 nan fliplr(1:1+length(t)-1)],4};count=count+1; % button outter circle
-fc{count}={1+length(t)*2:1+length(t)*3-1,5};count=count+1;  % top inner circle
-fc{count}={[1+length(t)*3:1+length(t)*4-1 nan fliplr(1+length(t)*2:1+length(t)*3-1)],6}; % top outter circle
-
-%% mesh generation of the cladding for the side-cut fiber
-%[node,elem,face]=s2m(no,face,1,50);
-[node,elem,face]=surf2mesh(no,fc,min(no),max(no),1,50,[0 0 1],[],0);
-
-plotmesh(no,fc,'y>-0.1');
-figure
-plotmesh(node,elem,'x>0 | y>0');
diff --git a/ext_libs/iso2mesh/sample/demo_grayscale_ex1.m b/ext_libs/iso2mesh/sample/demo_grayscale_ex1.m
deleted file mode 100755
index bbf667dc4..000000000
--- a/ext_libs/iso2mesh/sample/demo_grayscale_ex1.m
+++ /dev/null
@@ -1,28 +0,0 @@
-% this example demonstrates how to mesh a gray-scale volume directly.
-% the data set is a Jacobian matrix obtained by multiplying two
-% Green's functions
-% see Appendix in Qianqian Fang, Computational methods for microwave medical imaging. Ph.D.
-% Dissertation, Dartmouth College, Hanover, NH, U.S.A., Dec 2004.
-
-[xi,yi,zi]=meshgrid(1:40,1:40,1:80);
-r1=[xi(:)-20,yi(:)-20,zi(:)-20];
-r2=[xi(:)-20,yi(:)-20,zi(:)-60];
-r1=reshape(r1(:,1).^2+r1(:,2).^2+r1(:,3).^2,size(xi));
-r2=reshape(r2(:,1).^2+r2(:,2).^2+r2(:,3).^2,size(xi));
-
-k=10;
-
-% generate Green's functions
-
-g1=exp(sqrt(-1)*k*r1)./(4*pi*r1);
-g2=exp(sqrt(-1)*k*r2)./(4*pi*r2);
-
-
-%get Jacobian (sensitivity)
-g12=g1.*g2;
-
-% create a mesh based on the level-set at log(J)=-7.5
-
-[node,elem,face]=v2m(log10(abs(g12))+10,2.5,2,10,'cgalsurf');
-
-plotmesh(node,face);
diff --git a/ext_libs/iso2mesh/sample/demo_helloworld.m b/ext_libs/iso2mesh/sample/demo_helloworld.m
deleted file mode 100755
index a5b1bdcc9..000000000
--- a/ext_libs/iso2mesh/sample/demo_helloworld.m
+++ /dev/null
@@ -1,59 +0,0 @@
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% Hello World - The "getting started" example of iso2mesh
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-
-% In this example, we illustrate the basic mesh density and precision 
-% controls in iso2mesh.
-
-%% the first step is to load a binary or gray-scale image 
-
-hw=imread('helloworld.png');
-
-% now we stack the image and form a binary volume
-
-hw3d=1-repmat(hw,[1 1 50]);
-
-%% create 3D mesh          |--------> threshold at v=0.7
-[node,elem,face]=v2m(hw3d,0.7,5,40);
-%                             |  |-> maximum volume
-%                             |----> maximum surface triangle size
-
-figure;
-subplot(211);
-plotmesh(node,face);axis equal;view(90,60);
-subplot(212);
-plotmesh(node,elem,'z<20');axis equal;view(90,60);
-
-% mesh with denser surface    |----> surface triangle size is now 2
-[node,elem,face]=v2m(hw3d,0.7,2,40);
-
-figure;
-subplot(211);
-plotmesh(node,face);axis equal;view(90,60);
-subplot(212);
-plotmesh(node,elem,'z<20');axis equal;view(90,60);
-
-%% create 3D mesh from gray-scale image to get smoother boundary
-hw=imread('helloworld_gray.png');
-hw3d=255-repmat(hw,[1 1 50]);
-[node,elem,face]=v2m(hw3d,128,2,40);
-
-figure;
-subplot(211);
-plotmesh(node,face);axis equal;view(90,60);
-subplot(212);
-plotmesh(node,elem,'z<20');axis equal;view(90,60);
-
-%% create 3D mesh from gray-scale image with advanced distbound control
-clear opt
-opt.radbound=4;       % set surface triangle maximum size
-opt.distbound=0.2;    % set max distance that deviates from the level-set
-opt.autoregion=1;
-[node,elem,face]=v2m(hw3d,128,opt,40);
-
-figure;
-subplot(211);
-plotmesh(node,face);axis equal;view(90,60);
-subplot(212);
-plotmesh(node,elem,'z<20');axis equal;view(90,60);
-
diff --git a/ext_libs/iso2mesh/sample/demo_insert_nodes.m b/ext_libs/iso2mesh/sample/demo_insert_nodes.m
deleted file mode 100755
index bdcc8e0c1..000000000
--- a/ext_libs/iso2mesh/sample/demo_insert_nodes.m
+++ /dev/null
@@ -1,35 +0,0 @@
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%   demo script to insert new nodes to a tetrahedral mesh
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-
-load rat_head.mat
-
-[node,elem,face]=vol2mesh(volimage>0.05,1:size(volimage,1),1:size(volimage,2),...
-                           1:size(volimage,3),2,2,1);
-
-plotmesh(node,face);
-
-dt=pi/10;
-r=3;
-x0=30;
-y0=28;
-theta=dt:dt:2*pi;
-x=x0+r*cos(theta);
-y=y0+r*sin(theta);
-
-p0=[x;y;ones(1,length(theta))*50]';
-v0=[0,0,-1];
-
-[t,u,v,idx,xnode]=raysurf(p0,v0,node,face(:,1:3));
-
-hold on
-plotmesh(p0,'r+');
-
-goodpt=find(~isnan(xnode(:,1)) & ~isnan(xnode(:,2)) & ~isnan(xnode(:,3)));
-[newnode,newelem,newface]=meshrefine(node,elem,face,xnode(goodpt,:));
-
-figure
-plotmesh(newnode,newface);
-hold on
-plotmesh(p0,'r+');
-plotmesh(xnode,'r.')
diff --git a/ext_libs/iso2mesh/sample/demo_label_sizing.m b/ext_libs/iso2mesh/sample/demo_label_sizing.m
deleted file mode 100755
index 2bb1a2748..000000000
--- a/ext_libs/iso2mesh/sample/demo_label_sizing.m
+++ /dev/null
@@ -1,50 +0,0 @@
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% specify maximum cell sizes for different labels
-% (this is only valid when using 'cgalmesh' with v2m or vol2mesh)
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-
-% create a dummy image
-
-rad = 10:10:50;
-maxRad = max(rad);
-box = zeros(maxRad+1,maxRad+1,maxRad+1);
-image = box;
-box(1,1,1) = 1;
-%DT = bwdist(box,'euclidean');
-[ix,iy,iz]=meshgrid(1:maxRad+1,1:maxRad+1,1:maxRad+1);
-DT = sqrt((ix - 1).*(ix -1) + (iy - 1).*(iy -1) + (iz - 1).*(iz -1));
-
-for i = 1:size(rad,2)
-    ball = DT<=rad(i);
-    image(ball~=0) = image(ball~=0) + ball(ball~=0);
-end
-
-image = uint8(image);
-
-% mesh the domain with different sizing options
-
-figure;
-maxvol='1';
-[no,el]=v2m(image,[],5,maxvol,'cgalmesh');
-subplot(221);
-plotmesh(no(:,1:3),el,'x-y<0');
-title('a single scalar sets cell size for all labels');
-
-maxvol='1=2:2=1:3=2:4=1';
-[no,el]=v2m(image,[],5,maxvol,'cgalmesh');
-subplot(222);
-plotmesh(no(:,1:3),el,'x-y<0');
-title(sprintf('maxvol is "%s"',maxvol));
-
-maxvol='2:1:2:1';
-[no,el]=v2m(image,[],5,maxvol,'cgalmesh');
-subplot(224);
-plotmesh(no(:,1:3),el,'x-y<0');
-title(sprintf('maxvol is "%s", same as above',maxvol));
-
-maxvol='3=2:1:0.5';
-[no,el]=v2m(image,[],5,maxvol,'cgalmesh');
-subplot(223);
-plotmesh(no(:,1:3),el,'x-y<0');
-title(sprintf('maxvol is "%s", same to 3=2:4=1:5=0.5',maxvol));
-
diff --git a/ext_libs/iso2mesh/sample/demo_merge_surfaces.m b/ext_libs/iso2mesh/sample/demo_merge_surfaces.m
deleted file mode 100755
index 4745dc9fa..000000000
--- a/ext_libs/iso2mesh/sample/demo_merge_surfaces.m
+++ /dev/null
@@ -1,37 +0,0 @@
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%   Merge multiple surfaces and remove self-intersection elements
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-
-% generate a mesh for 
-load rat_head.mat
-[node0,face0]=v2s(volimage,0.5,2);
-
-c0=mean(meshcentroid(node0,face0(:,1:3)));
-c1=2*[18.5 20.7 20.9]-c0;
-
-[cnode,cface]=meshacylinder(c0,c1,4);
-[cnode,cface]=meshcheckrepair(cnode,cface(:,1:3));
-
-% combine two surfaces, producing 4 pieces of subsurfaces: surf 1
-% outside/inside of surf2 and surf2 outside/inside of surf1
-
-[no,el]=surfboolean(node0,face0(:,1:3),'all',cnode,cface);
-figure
-plotmesh(no,el,'y>20')
-
-% take the first surface only
-
-% el(:,4)==1: surf 1 outside of surf 2; el(:,4)==3: surf 1 inside of surf 2
-[no,el]=surfboolean(node0,face0(:,1:3),'first',cnode,cface);
-figure
-plotmesh(no,el)
-
-% the mesh after boolean operation can have self-intersecting elements, one
-% has to fix those defects before passing to s2m
-
-[no1,el1]=meshcheckrepair(no(:,1:3),el(:,1:3));
-
-%ISO2MESH_TETGENOPT=' -A -q 0.8 -a 10 ';
-[node,elem,face]=s2m(no1,el1,1,10);
-figure;
-plotmesh(node,face)
diff --git a/ext_libs/iso2mesh/sample/demo_mesh_smoothing.m b/ext_libs/iso2mesh/sample/demo_mesh_smoothing.m
deleted file mode 100755
index 9c2a7a479..000000000
--- a/ext_libs/iso2mesh/sample/demo_mesh_smoothing.m
+++ /dev/null
@@ -1,110 +0,0 @@
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%   demo script for surface smoothing
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-
-%% preparation
-% user must add the path of iso2mesh to matlab path list
-% addpath('../');
-
-% user need to add the full path to .../iso2mesh/bin directory
-% to windows/Linux/Unix PATH environment variable
-
-%% load the sample data
-load rat_head.mat
-
-% volimage is a volumetric image such as an X-ray or MRI image
-% A,b are registration matrix and vector, respectively
-%% perform mesh generation
-
-[node,face]=v2s(volimage,0.5,2,'cgalmesh');
-
-face=face(:,1:3);
-
-p0=min(node);
-p1=max(node);
-
-rownum=3;
-colnum=4;
-figure;
-subplot(rownum,colnum,1);
-
-plotmesh(node,face(:,1:3));
-if(~isoctavemesh) 
-	title({'Laplacian+HC Smoothing Test','no smoothing'}); 
-else
-	title('Laplacian+HC - no smoothing');
-end
-axis equal;
-set(gca,'xlim',[p0(1),p1(1)],'ylim',[p0(2),p1(2)],'zlim',[p0(3),p1(3)])
-
-%=========================================================
-% apply Laplacian+HC smoothing
-%=========================================================
-
-n1=node;
-for i=1:rownum*colnum-1
-  n1=sms(n1,face(:,1:3),1,0.5); % apply Laplacian+HC mesh smoothing
-  subplot(rownum,colnum,i+1);
-  plotmesh(n1,face(:,1:3));
-  title(['iter=' num2str(i)]);
-  axis equal;
-  set(gca,'xlim',[p0(1),p1(1)],'ylim',[p0(2),p1(2)],'zlim',[p0(3),p1(3)])
-end
-
-%=========================================================
-% apply Laplacian smoothing
-%=========================================================
-
-figure;
-subplot(rownum,colnum,1);
-
-plotmesh(node,face(:,1:3));
-if(~isoctavemesh)
-        title({'Laplacian Smoothing Test','no smoothing'});
-else
-        title('Laplacian - no smoothing');
-end
-axis equal;
-set(gca,'xlim',[p0(1),p1(1)],'ylim',[p0(2),p1(2)],'zlim',[p0(3),p1(3)])
-
-conn=meshconn(face(:,1:3),size(node,1));
-
-n1=node;
-for i=1:rownum*colnum-1
-  n1=smoothsurf(n1,[],conn,1,0.5,'laplacian');
-  subplot(rownum,colnum,i+1);
-  plotmesh(n1,face(:,1:3));
-  title(['iter=' num2str(i)]);
-  axis equal;
-  set(gca,'xlim',[p0(1),p1(1)],'ylim',[p0(2),p1(2)],'zlim',[p0(3),p1(3)])
-end
-
-
-%=========================================================
-% apply Low-pass smoothing
-%=========================================================
-
-figure;
-subplot(rownum,colnum,1);
-
-plotmesh(node,face(:,1:3));
-if(~isoctavemesh)
-        title({'Low-pass Smoothing Test','no smoothing'});
-else
-        title('Low-pass - no smoothing');
-end
-axis equal;
-set(gca,'xlim',[p0(1),p1(1)],'ylim',[p0(2),p1(2)],'zlim',[p0(3),p1(3)])
-
-conn=meshconn(face(:,1:3),size(node,1));
-
-n1=node;
-for i=1:rownum*colnum-1
-  n1=smoothsurf(n1,[],conn,1,0.5,'lowpass');
-  subplot(rownum,colnum,i+1);
-  plotmesh(n1,face(:,1:3));
-  title(['iter=' num2str(i)]);
-  axis equal;
-  set(gca,'xlim',[p0(1),p1(1)],'ylim',[p0(2),p1(2)],'zlim',[p0(3),p1(3)])
-end
-
diff --git a/ext_libs/iso2mesh/sample/demo_qmeshcut_ex1.m b/ext_libs/iso2mesh/sample/demo_qmeshcut_ex1.m
deleted file mode 100755
index 75390ce00..000000000
--- a/ext_libs/iso2mesh/sample/demo_qmeshcut_ex1.m
+++ /dev/null
@@ -1,79 +0,0 @@
-% qmeshcut demonstration
-%
-% by Qianqian Fang, <fangq at nmr.mgh.harvard.edu>
-%
-% to demonstrate how to use qmeshcut to produce cross-sectional plot 
-% of an un-structured (tetrahedral) mesh
-
-% run vol2mesh demo 1 to create a 3d mesh
-
-demo_vol2mesh_ex1
-
-% define a plane by 3 points, in this case, z=mean(node(:,3))
-
-z0=mean(node(:,3));
-
-plane=[min(node(:,1)) min(node(:,2)) z0
-       min(node(:,1)) max(node(:,2)) z0
-       max(node(:,1)) min(node(:,2)) z0];
-
-% run qmeshcut to get the cross-section information at z=mean(node(:,1))
-% use the x-coordinates as the nodal values
-
-[cutpos,cutvalue,facedata]=qmeshcut(elem(:,1:4),node,node(:,1),plane);
-
-% plot your results
-
-figure;
-hsurf=trimesh(face(:,1:3),node(:,1),node(:,2),node(:,3),'facecolor','none');
-hold on;
-if(isoctavemesh)
-  hcut=patch('Faces',facedata,'Vertices',cutpos);
-else
-  hcut=patch('Faces',facedata,'Vertices',cutpos,'FaceVertexCData',cutvalue,'facecolor','interp');
-end
-%set(hcut, 'linestyle','none')
-axis equal;
-
-% qmeshcut can also cut a surface
-
-[bcutpos,bcutvalue,bcutedges]=qmeshcut(face(:,1:3),node,node(:,1),plane);
-[bcutpos,bcutedges]=removedupnodes(bcutpos,bcutedges);
-bcutloop=extractloops(bcutedges);
-
-bcutloop(isnan(bcutloop))=[]; % there can be multiple loops, remove the separators
-
-% plot the plane-surface cuts
-
-plot3(bcutpos(bcutloop,1),bcutpos(bcutloop,2),bcutpos(bcutloop,3),'r','LineWidth',4);
-
-% essencially, this should be the same as you do a removedupnodes(cutpos,facedata)
-% and then call extractloop(facedata)
-
-
-% qmeshcut can also cut along an isosurface
-
-% define a field over the mesh: sensitivity map from a source/detector pair
-
-r1=[node(:,1)-20,node(:,2)-25,node(:,3)-25];
-r2=[node(:,1)-10,node(:,2)-25,node(:,3)-14];
-r1=sqrt(r1(:,1).^2+r1(:,2).^2+r1(:,3).^2);
-r2=sqrt(r2(:,1).^2+r2(:,2).^2+r2(:,3).^2);
-
-k=10;
-g1=exp(sqrt(-1)*k*r1)./(4*pi*r1); % calculate the Green's function
-g2=exp(sqrt(-1)*k*r2)./(4*pi*r2);
-g12=g1.*g2;  % this is the sensitivity map
-
-figure
-plotmesh([node log10(abs(g12))],elem,'facealpha',0.5,'linestyle','none'); % plot the mesh
-
-hold on;
-% cut the mesh at value=-4
-[cutpos,cutvalue,facedata]=qmeshcut(elem(:,1:4),node(:,1:3),log10(abs(g12)),-4); 
-patch('Vertices',cutpos,'Faces',facedata,'FaceVertexCData',cutvalue,'FaceColor','interp');
-
-% cut the mesh at value=-4.5
-[cutpos,cutvalue,facedata]=qmeshcut(elem(:,1:4),node(:,1:3),log10(abs(g12)),-4.5);
-patch('Vertices',cutpos,'Faces',facedata,'FaceVertexCData',cutvalue,'FaceColor','interp');
-
diff --git a/ext_libs/iso2mesh/sample/demo_refine_spherebox_mesh.m b/ext_libs/iso2mesh/sample/demo_refine_spherebox_mesh.m
deleted file mode 100755
index f7a2d817b..000000000
--- a/ext_libs/iso2mesh/sample/demo_refine_spherebox_mesh.m
+++ /dev/null
@@ -1,72 +0,0 @@
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%  Create meshes for a sphere inside a cubic domain
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-
-% preparation
-
-% you have to add the path to iso2mesh toolbox 
-% addpath('/path/to/iso2mesh/toolbox/');
-
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%  Part 0.  Create a Spherical Mesh
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-
-[no,el]=meshasphere([30 30 30],20,2.5);
-
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%  Part I.  A Coarse Mesh for a Sphere Inside a Box with Refinement
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-
-% generate a coarse volumetric mesh from the sphere with an additional bounding box
-% the maximum element volume is 8
-
-ISO2MESH_SESSION='demo_sph3_';
-
-srcpos=[30. 30. 0.];                     % set the center of the ROI
-fixednodes=[30.,30.,0.1; 30 30 30];     % add control points so we can refine mesh densities there
-nodesize=[ones(size(no,1),1) ; 0.2; 4];  % set target edge size of 1 for all nodes on the sphere
-                                         % target edge size 0.3 near (30,30,0.05)
-                                         % and target edge size 4 near (30,30,30)
-nfull=[no;fixednodes];                   % append additional control points
-[node3,elem3,face3]=surf2mesh([nfull,nodesize],el,[0 0 0],[61 61 61],1,8,[30 30 30],[],[2 2 2 2 6 6 6 6]);
-                             % ^- add node size as the last            ^ max volume     ^- edge sizes at the 8 
-                             %    column to node                                           corners of the bounding box
-[node3,elem3,face3]=sortmesh(srcpos,node3,elem3,1:4,face3,1:3);  % reorder the nodes/elements 
-                                                 % so that the nodes near earch order
-                                                 % are more clustered in the memory
-elem3(:,1:4)=meshreorient(node3,elem3(:,1:4));   % reorient elements to ensure the volumns are positive
-
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%  Part II.  A Dense Mesh for a Sphere Inside a Box with Refinement
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% generate a dense volumetric mesh from the sphere with an additional bounding box
-% the maximum element volume is 2
-
-ISO2MESH_SESSION='demo_sph2_';
-
-nodesize=[0.7*ones(size(no,1),1) ; 0.2; 2];  % set target edge size to 0.7 near the sphere
-                                             % 0.2 near (30,30,0.5) and 2 near (30,30,30)
-[node2,elem2,face2]=surf2mesh([nfull,nodesize],el,[0 0 0],[61 61 61],1,2,[30 30 30],[],[1 1 1 1 5 5 5 5]);
-
-figure; plotmesh(node2,face2(:,1:3),'y>30');axis equal;
-
-[node2,elem2,face2]=sortmesh(srcpos,node2,elem2,1:4,face2,1:3);
-elem2(:,1:4)=meshreorient(node2,elem2(:,1:4));
-
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%  Part III.  A Coarse Mesh for a Sphere Inside a Box without Refinement
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-
-ISO2MESH_SESSION='demo_sph1_';
-
-% reduce the surface node numbers to 20%  
-[no2,el2]=meshresample(no,el,0.2);  % down sample the sphere mesh
-
-% using the coarse spherical surface, we generate a coarse volumetric
-% mesh with maximum volume of 10
-
-[node1,elem1,face1]=surf2mesh(no2,el2,[0 0 0],[61 61 61],1,10,[30 30 30],[],1);
-[node1,elem1,face1]=sortmesh(srcpos,node1,elem1,1:4,face1,1:3);
-elem1(:,1:4)=meshreorient(node1,elem1(:,1:4));
-
-clear ISO2MESH_SESSION
diff --git a/ext_libs/iso2mesh/sample/demo_remesh_surface.m b/ext_libs/iso2mesh/sample/demo_remesh_surface.m
deleted file mode 100755
index a0ba8a27a..000000000
--- a/ext_libs/iso2mesh/sample/demo_remesh_surface.m
+++ /dev/null
@@ -1,33 +0,0 @@
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%   demo script for surface repairing using surf2vol and remeshsurf
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-
-%% preparation
-% user must add the path of iso2mesh to matlab path list
-% addpath('../');
-
-% user need to add the full path to .../iso2mesh/bin directory
-% to windows/Linux/Unix PATH environment variable
-
-%% load the sample data
-load rat_head.mat
-
-% volimage is a volumetric image such as an X-ray or MRI image
-% A,b are registration matrix and vector, respectively
-%% perform mesh generation
-
-[node,face]=v2s(volimage,0.5,2,'cgalmesh');
-
-node=node(:,1:3);
-face=face(:,1:3);
-
-plotmesh(node,face);
-axis equal
-
-[newno,newfc]=remeshsurf(node,face,1);
-
-newno=sms(newno,newfc(:,1:3),3,0.5);
-
-figure;
-plotmesh(newno,newfc(:,1:3));
-axis equal
diff --git a/ext_libs/iso2mesh/sample/demo_shortcut_ex1.m b/ext_libs/iso2mesh/sample/demo_shortcut_ex1.m
deleted file mode 100755
index 3021b7800..000000000
--- a/ext_libs/iso2mesh/sample/demo_shortcut_ex1.m
+++ /dev/null
@@ -1,39 +0,0 @@
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%   demo script for using short-hand version of the meshing wrappers
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-
-%% preparation
-% user must add the path of iso2mesh to matlab path list
-% addpath('../');
-
-% user need to add the full path to .../iso2mesh/bin directory
-% to windows/Linux/Unix PATH environment variable
-
-%% load the sample data
-load rat_head.mat
-
-% volimage is a volumetric image such as an X-ray or MRI image
-%% v2m is the short-hand version of vol2mesh
-
-% mesh volimage at threshold level 0.05, max surface element size 3,
-% maximum tetrahedral element volume 2
-
-[node,elem,face]=v2m(volimage,0.05,3,2);
-
-%% visualize the resulting mesh
-subplot(211);
-plotmesh(node,face);
-axis equal;
-
-%% alternatively, one can call vol2surf and surf2mesh separately
-
-% v2s: shorthand version of vol2surf, s2m: shorthand version of surf2mesh
-
-[node,face,regions,holes]=v2s(volimage,0.05,3);
-[node,elem,face]=s2m(node,face,1,2);
-
-%% visualize the resulting mesh
-subplot(212)
-plotmesh(node,face);
-axis equal;
-
diff --git a/ext_libs/iso2mesh/sample/demo_surf2mesh_ex1.m b/ext_libs/iso2mesh/sample/demo_surf2mesh_ex1.m
deleted file mode 100755
index ad09ae379..000000000
--- a/ext_libs/iso2mesh/sample/demo_surf2mesh_ex1.m
+++ /dev/null
@@ -1,21 +0,0 @@
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%   demo script for mesh generation from surface patches and bounding box
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-
-%% preparation
-% user must add the path of iso2mesh to matlab path list
-% addpath('../');
-
-% user need to add the full path to .../iso2mesh/bin directory
-% to windows/Linux/Unix PATH environment variable
-
-%% load the sample data
-load tube_surface.mat
-
-% f and v stores the surface patch faces and nodes
-%% perform mesh generation
-[node,elem,face]=surf2mesh(v,f,[1 1 1],[100 100 100],0.1,25);
-
-%% visualize the resulting mesh
-plotmesh(node,face(:,1:3));
-axis equal;
diff --git a/ext_libs/iso2mesh/sample/demo_surf2vol_ex1.m b/ext_libs/iso2mesh/sample/demo_surf2vol_ex1.m
deleted file mode 100755
index 49812a34c..000000000
--- a/ext_libs/iso2mesh/sample/demo_surf2vol_ex1.m
+++ /dev/null
@@ -1,60 +0,0 @@
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%   demo script to convert a closed surface to a binary image
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-
-%% preparation
-% user must add the path of iso2mesh to matlab path list
-% addpath('../');
-
-%% load the sample data
-load rat_head.mat
-
-% first, generate a surface from the original image
-% similar to demo_shortcuts_ex1.m
-
-[node,face,regions,holes]=v2s(volimage,0.5,3);
-
-node=sms(node,face(:,1:3),3,0.5); % apply 3 mesh smoothing
-
-mdim=ceil(max(node)+1);
-dstep=0.25;
-zslice=15;
-xrange=0:dstep:mdim(1);
-yrange=0:dstep:mdim(2);
-zrange=0:dstep:mdim(3);
-img=surf2vol(node,face(:,1:3),xrange,yrange,zrange);
-
-imagesc(squeeze(img(:,:,zslice))); % z=10
-
-hold on
-
-z0=zslice*dstep;
-plane=[min(node(:,1)) min(node(:,2)) z0
-       min(node(:,1)) max(node(:,2)) z0
-       max(node(:,1)) min(node(:,2)) z0];
-
-% run qmeshcut to get the cross-section information at z=mean(node(:,1))
-% use the x-coordinates as the nodal values
-
-[bcutpos,bcutvalue,bcutedges]=qmeshcut(face(:,1:3),node,node(:,1),plane);
-[bcutpos,bcutedges]=removedupnodes(bcutpos,bcutedges);
-bcutloop=extractloops(bcutedges);
-bcutloop(isnan(bcutloop))=[]; % there can be multiple loops, remove the separators
-plot(bcutpos(bcutloop,2)*(1/dstep),bcutpos(bcutloop,1)*(1/dstep),'w');
-
-if(isoctavemesh)
-  if(~exist('bwfill'))
-    error('you need to install octave-image toolbox first');
-  end
-  img2=zeros(size(img),'uint8');
-  for i=1:size(img,3)
-    img2(:,:,i)=bwfill(img(:,:,i),'holes');
-  end
-  img2=img2+img;
-else
-  img2=imfill(img,'holes')+img;
-end
-figure;
-imagesc(squeeze(img2(:,:,zslice))); % z=10
-hold on;
-plot(bcutpos(bcutloop,2)*(1/dstep),bcutpos(bcutloop,1)*(1/dstep),'y--');
diff --git a/ext_libs/iso2mesh/sample/demo_vol2mesh_ex1.m b/ext_libs/iso2mesh/sample/demo_vol2mesh_ex1.m
deleted file mode 100755
index 54e9ec48e..000000000
--- a/ext_libs/iso2mesh/sample/demo_vol2mesh_ex1.m
+++ /dev/null
@@ -1,29 +0,0 @@
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%   demo script for mesh generation from binarized volumetric image
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-
-%% preparation
-% user must add the path of iso2mesh to matlab path list
-% addpath('../');
-
-% user need to add the full path to .../iso2mesh/bin directory
-% to windows/Linux/Unix PATH environment variable
-
-%% load the sample data
-load rat_head.mat
-
-% volimage is a volumetric image such as an X-ray or MRI image
-% A,b are registration matrix and vector, respectively
-%% perform mesh generation
-
-[node,elem,face]=vol2mesh(volimage>0.05,1:size(volimage,1),1:size(volimage,2),...
-                           1:size(volimage,3),2,2,1);
-
-%% alternatively, one can use the following cmd as a less robust approach
-% [node,elem,face]=vol2mesh(volimage>0.05,1:size(volimage,1),1:size(volimage,2),...
-%                           1:size(volimage,3),0.2,2,1,'simplify');
-
-%% visualize the resulting mesh
-
-plotmesh(node,face);
-axis equal;
diff --git a/ext_libs/iso2mesh/sample/demo_vol2mesh_ex1b.m b/ext_libs/iso2mesh/sample/demo_vol2mesh_ex1b.m
deleted file mode 100755
index cb54b2d3d..000000000
--- a/ext_libs/iso2mesh/sample/demo_vol2mesh_ex1b.m
+++ /dev/null
@@ -1,30 +0,0 @@
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%   demo script for mesh generation from binarized volumetric image
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-
-%% preparation
-% user must add the path of iso2mesh to matlab path list
-% addpath('../');
-
-% user need to add the full path to .../iso2mesh/bin directory
-% to windows/Linux/Unix PATH environment variable
-
-%% load the sample data
-load rat_head.mat
-
-% volimage is a volumetric image such as an X-ray or MRI image
-% A,b are registration matrix and vector, respectively
-%% perform mesh generation
-
-%% use the alternative 'simplify' method: first create voxel-based
-% surface mesh, and then resample it to desired density.
-% this method does not guarantee to be free of self-intersecting
-% element, as 'cgalsurf' promises.
-
-[node,elem,face]=vol2mesh(volimage>0.05,1:size(volimage,1),1:size(volimage,2),...
-                          1:size(volimage,3),0.1,2,1,'simplify');
-
-%% visualize the resulting mesh
-
-plotmesh(node,face);
-axis equal;
diff --git a/ext_libs/iso2mesh/sample/demo_vol2mesh_ex1c.m b/ext_libs/iso2mesh/sample/demo_vol2mesh_ex1c.m
deleted file mode 100755
index 0f05ee3b3..000000000
--- a/ext_libs/iso2mesh/sample/demo_vol2mesh_ex1c.m
+++ /dev/null
@@ -1,30 +0,0 @@
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%   demo script for mesh generation from binary volumetric image
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-
-%% preparation
-% user must add the path of iso2mesh to matlab path list
-% addpath('../');
-
-% user need to add the full path to .../iso2mesh/bin directory
-% to windows/Linux/Unix PATH environment variable
-
-%% load the sample data
-load rat_head.mat
-
-% volimage is a volumetric image such as an X-ray or MRI image
-% A,b are registration matrix and vector, respectively
-%% perform mesh generation
-
-%% use the alternative 'cgalmesh' method. This will call 
-% cgalmesher to process labled volume to produce surfaces
-% and tetrahedral mesh in a single run.
-clear opt
-opt.radbound=2;
-[node,elem,face]=v2m(uint8(volimage),0.5,opt,100,'cgalmesh');
-
-
-%% visualize the resulting mesh
-
-plotmesh(node,face(:,1:3));
-axis equal;
diff --git a/ext_libs/iso2mesh/sample/demo_vol2mesh_ex2.m b/ext_libs/iso2mesh/sample/demo_vol2mesh_ex2.m
deleted file mode 100755
index 0dc0493f9..000000000
--- a/ext_libs/iso2mesh/sample/demo_vol2mesh_ex2.m
+++ /dev/null
@@ -1,24 +0,0 @@
-% sample script to create volumetric mesh from 
-% multiple levelsets of a binary segmented head image.
-%
-% Author: Qianqian Fang <fangq at nmr.mgh.harvard.edu>
-
-% load iso2mesh image
-
-img=imread('iso2mesh_bar.tif');
-img=fliplr(img);
-fullimg=repmat(1-img,[1,1,30]);
-fullimg(:,:,31:60)=repmat(ones(size(img)),[1,1,30]);
-
-% create volumetric tetrahedral mesh from the two-layer 3D images
-% this may take another few minutes for a 256x256x256 volume
-clear opt
-opt.keepratio=0.1; % this option is only useful when vol2mesh uses 'simplify' method
-opt.radbound=3;    % set the target surface mesh element bounding sphere be <3 pixels in radius.
-tic
-[node,elem,face]=vol2mesh(fullimg,1:size(fullimg,1),1:size(fullimg,2),1:size(fullimg,3),opt,100,1);
-toc
-
-hb=plotmesh(node,face);
-axis equal
-view(-90.5,-72);
diff --git a/ext_libs/iso2mesh/sample/demo_vol2mesh_ex3.m b/ext_libs/iso2mesh/sample/demo_vol2mesh_ex3.m
deleted file mode 100755
index e26d67d68..000000000
--- a/ext_libs/iso2mesh/sample/demo_vol2mesh_ex3.m
+++ /dev/null
@@ -1,53 +0,0 @@
-% sample script to create volumetric mesh from 
-% multiple levelsets of a binary segmented head image.
-%
-% Author: Qianqian Fang <fangq at nmr.mgh.harvard.edu>
-
-% load full head image (T1 MRI scan)
-
-fprintf(1,'loading binary head image...\n');
-for i=1:256 
-  head(:,:,i)=imread('head.tif',i);
-end
-
-% load segmented brain images (by freesurfer recon_all)
-fprintf(1,'loading binary brain image...\n');
-for i=1:256
-  brain(:,:,i)=imread('brain.tif',i);
-end
-
-% fill holes in the head image and create the canonical binary volume
-% this may take a few minutes for a 256x256x256 volume
-fprintf(1,'filling holes in the volumetric images...\n');
-tic
-cleanimg=fillholes3d(logical(head>0),10);
-cleanbrain=fillholes3d(logical(brain>0),10);
-toc
-
-% add brain image as additional segment
-cleanimgfull=cleanimg+(cleanbrain>0);
-
-% create volumetric tetrahedral mesh from the two-layer 3D images
-% this may take another few minutes for a 256x256x256 volume
-clear opt;
-
-% set method for vol2mesh to 'simplify' to use these option
-opt(1).keepratio=0.05; % resample levelset 1 to 5%  
-opt(2).keepratio=0.1;  % resample levelset 2 to 10%
-
-% by default, vol2mesh uses 'cgalsurf' method, which requires the following
-opt(1).radbound=4; % head surface element size bound
-opt(2).radbound=2; % brain surface element size bound
-opt(1).side='lower'; %
-opt(2).side='lower'; %
-
-tic
-[node,elem,face]=vol2mesh(cleanimgfull,1:size(cleanimg,1),1:size(cleanimg,2),1:size(cleanimg,3),opt,100,1);
-toc
-
-% plot the boundary surface of the generated mesh
-h=slice(cleanimgfull,[],[120],[120 180]);
-set(h,'linestyle','none')
-hold on
-
-plotmesh(node(:,[2 1 3]),face,'facealpha',0.7);
diff --git a/ext_libs/iso2mesh/sample/head.tif b/ext_libs/iso2mesh/sample/head.tif
deleted file mode 100755
index d5011af6d..000000000
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diff --git a/ext_libs/iso2mesh/sample/iso2mesh_bar.tif b/ext_libs/iso2mesh/sample/iso2mesh_bar.tif
deleted file mode 100755
index cf4b06c85..000000000
Binary files a/ext_libs/iso2mesh/sample/iso2mesh_bar.tif and /dev/null differ