New release (v1.0.20190902)

README.md

@@ -4,7 +4,7 @@
 
 Surf Ice is an open source surface render. It can be compiled for the Linux, Macintosh OSX, and Windows operating systems. For details and compiled versions visit the [NITRC wiki](https://www.nitrc.org/plugins/mwiki/index.php/surfice:MainPage). You can also get a compiled version from the [Github releases page](https://github.com/neurolabusc/surf-ice/releases).
 
-Supported mesh formats include 3DO, 3DS, AC, BYU, CTM, DAE, DXF, FreeSurfer, GII (GIfTI), GTS, LWO2, MS3D, MZ3, NV (BrainNetViewer), OBJ, OFF, PLY, PLY2, STL, VTK, WFR. Online converters can convert meshes from other formats to one of these. Tractography formats include BFloat, PDB, TCK, TRK, and VTK. The software supports the NIfTI voxelwise format (tools like dcm2niix can help convert other voxel-based formats to NIfTI).
+Supported mesh formats include 3DO, 3DS, AC, BYU, CTM, DAE, DXF, FreeSurfer, GII (GIfTI), GTS, LWO2, MS3D, MZ3, NV (BrainNetViewer), OBJ, OFF, PLY, PLY2, STL, VTK, WFR. Online converters can convert meshes from other formats to one of these. Tractography formats include BFloat, PDB, TCK, TRK, and VTK. Supported volume formats include those supported by [i2nii](https://github.com/rordenlab/i2nii): AFNI Brik(.head), Analyze(.hdr), Bio-Rad PIC(.pic), Blender Voxel data(.bvox), BrainVoyager VMR(.vmr, .v16), DeltaVision(.dv), ECAT(.v), FreeSurfer MGH/MGZ Volume(.mgh/.mgz), Guys Image Processing Lab(.gipl), ICS Image Cytometry Standard(.ics), Interfile(.varies, limited support), ITK MHA/MHD(.mha/.mhd), MRTrix Volume(.mif/.mih; not all variants supported), NIfTI(.hdr/.nii/.nii.gz/.voi), NRRD(.nhdr/.nrrd), POV-Ray Density_File(.df3), Spectroscopic Imaging, Visualization and Computing (SIVIC)(.idf), Stimulate Sdt(.spr/.sdt), Vaa3D(.v3draw), VTK Legacy Voxel Format(.vtk). Tools like [dcm2niix](https://github.com/rordenlab/dcm2niix) can help convert voxel-based DICOM images to NIfTI.
 
 ![alt tag](https://github.com/neurolabusc/surf-ice/blob/master/Surfice.jpg)
 

Resources/matcap/license.txt

@@ -3,14 +3,8 @@ with regards to mc01.jpg...mc24.jpg
  These matcap images are licensed as GNU GPL 2 or later, like the rest of Blender's code.
  Thanks to Kent Trammell, Aidy Burrows, John Herreno , Terry Wallwork and David Silverman for making the pictures.
 
-carpaint from
- https://blog.mikepan.com/post/137759885931/realistic-car-paint-brdf-material
-
 with regards to fubax.jpg
  https://github.com/Fubaxiusz/fubax-shaders/blob/master/Textures/matcap.png
 
-cortex and red plastic matcaps from
- http://www.alecjacobson.com/weblog/?p=4827
-
-remaining matcaps from
- https://devtalk.blender.org/t/call-for-content-matcaps/737/203
+Porcelain from
+ https://threejs.org/examples/webgl_materials_matcap.html

Resources/script/matcap.gls

@@ -0,0 +1,12 @@
+begin
+	resetdefaults();
+	meshload('BrainMesh_ICBM152Right.mz3');
+	overlayload('motor_4t95mesh.mz3');
+	overlaycolorname(1, 'red');
+	shaderxray(0.9, 0.5);
+	azimuthelevation(110, 15);
+	meshcurv();
+	shadername('MatCap');
+	shadermatcap('MetalShiny');
+end.
+

Resources/script/matcapMesh.py

@@ -0,0 +1,11 @@
+import gl
+gl.resetdefaults()
+gl.meshload('BrainMesh_ICBM152Right.mz3')
+gl.overlayload('motor_4t95mesh.mz3')
+gl.overlaycolorname(1, 'red')
+gl.shaderxray(0.9, 0.5)
+gl.azimuthelevation(110, 15)
+gl.shadername('MatCap');
+gl.shadermatcap('Cortex');
+gl.meshcurv()
+gl.overlaytranslucent(2, 1)

Resources/script/matcapPainted.py

@@ -0,0 +1,12 @@
+import gl
+gl.resetdefaults()
+gl.meshload('BrainMesh_ICBM152Right.mz3')
+gl.overlayload('motor_4t95vol.nii.gz')
+gl.overlayminmax(1,2,12)
+gl.overlaycolorname(2, 'Red-Yellow')
+gl.azimuthelevation(110, 15)
+gl.shadername('MatCap');
+gl.meshcurv()
+gl.overlaytranslucent(2, 1)
+
+

Resources/script/matcapSubcortical.py

@@ -0,0 +1,7 @@
+import gl
+gl.resetdefaults()
+gl.meshload('mni152_2009AO.mz3')
+gl.overlayload('CIT168.mz3')
+gl.shadername('MatCap')
+gl.shadermatcap('Cortex')
+gl.shaderxray(1.0, 0.9)

Resources/script/overlap.gls

@@ -0,0 +1,13 @@
+begin
+	resetdefaults();
+	azimuthelevation(70, 15);
+	meshload('BrainMesh_ICBM152Right.mz3');
+	overlayload('ICBM152_Right_ROI.mz3');
+	overlayload('motor_4t95vol.nii.gz');
+	overlayminmax(2,4,4);
+	overlaycolorname(2, 'Red');
+	meshcurv();
+	//next line determines if the motor overlay hides the region of interest
+	overlayoverlapoverwrite(true);
+end.
+