Extraction of Mesh from FreeSurfer
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1 Extraction of Mesh from FreeSurfer Lars Magnus Valnes University of Oslo March 4, 2016 Lars Magnus Valnes (UiO) FreeSurfer March 4, / 20
2 Introduction Goals We some goals for today : Lars Magnus Valnes (UiO) FreeSurfer March 4, / 20
3 Introduction Goals We some goals for today : Basic understanding of FreeSurfer Lars Magnus Valnes (UiO) FreeSurfer March 4, / 20
4 Introduction Goals We some goals for today : Basic understanding of FreeSurfer Know how to extract a binary surface file from FreeSurfer. Lars Magnus Valnes (UiO) FreeSurfer March 4, / 20
5 Introduction Goals We some goals for today : Basic understanding of FreeSurfer Know how to extract a binary surface file from FreeSurfer. Construction of a mesh with mshr. Lars Magnus Valnes (UiO) FreeSurfer March 4, / 20
6 Introduction Some basic things about FreeSurfer. Lars Magnus Valnes (UiO) FreeSurfer March 4, / 20
7 Introduction Some basic things about FreeSurfer. FreeSurfer is a set of software tools for the study of cortical and subcortical anatomy structures. Lars Magnus Valnes (UiO) FreeSurfer March 4, / 20
8 Introduction Some basic things about FreeSurfer. FreeSurfer is a set of software tools for the study of cortical and subcortical anatomy structures. Most of FreeSurfer is automated. Thus simple to use, but not to debug. Lars Magnus Valnes (UiO) FreeSurfer March 4, / 20
9 Introduction Some basic things about FreeSurfer. FreeSurfer is a set of software tools for the study of cortical and subcortical anatomy structures. Most of FreeSurfer is automated. Thus simple to use, but not to debug. The code written in C and based on ITK (National Library of Medicine Insight Segmentation and Registration Toolkit). Lars Magnus Valnes (UiO) FreeSurfer March 4, / 20
10 Setting up FreeSurfer Lars Magnus Valnes (UiO) FreeSurfer March 4, / 20
11 Setting up FreeSurfer Download from here and obtain license.txt here Lars Magnus Valnes (UiO) FreeSurfer March 4, / 20
12 Setting up FreeSurfer Download from here and obtain license.txt here FreeSurfer require that we set some environment variables. Lars Magnus Valnes (UiO) FreeSurfer March 4, / 20
13 Setting up FreeSurfer Download from here and obtain license.txt here FreeSurfer require that we set some environment variables. This can be done by modifying.bashrc or.tcshrc. Lars Magnus Valnes (UiO) FreeSurfer March 4, / 20
14 Setting up FreeSurfer Download from here and obtain license.txt here FreeSurfer require that we set some environment variables. This can be done by modifying.bashrc or.tcshrc. Two useful environment variables to know are: Lars Magnus Valnes (UiO) FreeSurfer March 4, / 20
15 Setting up FreeSurfer Download from here and obtain license.txt here FreeSurfer require that we set some environment variables. This can be done by modifying.bashrc or.tcshrc. Two useful environment variables to know are: $FREESURFER HOME $SUBJECTS DIR Lars Magnus Valnes (UiO) FreeSurfer March 4, / 20
16 Running FreeSurfer The first step is to input the MRIs to FreeSurfer, this is done by typing: Lars Magnus Valnes (UiO) FreeSurfer March 4, / 20
17 Running FreeSurfer The first step is to input the MRIs to FreeSurfer, this is done by typing: $recon-all -subjid NAME -i PATH2MRI Lars Magnus Valnes (UiO) FreeSurfer March 4, / 20
18 Running FreeSurfer The first step is to input the MRIs to FreeSurfer, this is done by typing: $recon-all -subjid NAME -i PATH2MRI Here NAME refers to what you want the folder in $SUBJECT DIR to be named, and it will store all the output related to the MRI. Lars Magnus Valnes (UiO) FreeSurfer March 4, / 20
19 Running FreeSurfer The first step is to input the MRIs to FreeSurfer, this is done by typing: $recon-all -subjid NAME -i PATH2MRI Here NAME refers to what you want the folder in $SUBJECT DIR to be named, and it will store all the output related to the MRI. PATH2MRI refers to the complete path to a nifti file or a single DICOM file in a serie. Lars Magnus Valnes (UiO) FreeSurfer March 4, / 20
20 Running FreeSurfer The first step is to input the MRIs to FreeSurfer, this is done by typing: $recon-all -subjid NAME -i PATH2MRI Here NAME refers to what you want the folder in $SUBJECT DIR to be named, and it will store all the output related to the MRI. PATH2MRI refers to the complete path to a nifti file or a single DICOM file in a serie. The next step is to type : Lars Magnus Valnes (UiO) FreeSurfer March 4, / 20
21 Running FreeSurfer The first step is to input the MRIs to FreeSurfer, this is done by typing: $recon-all -subjid NAME -i PATH2MRI Here NAME refers to what you want the folder in $SUBJECT DIR to be named, and it will store all the output related to the MRI. PATH2MRI refers to the complete path to a nifti file or a single DICOM file in a serie. The next step is to type : $recon-all -subjid NAME -all Lars Magnus Valnes (UiO) FreeSurfer March 4, / 20
22 Running FreeSurfer The first step is to input the MRIs to FreeSurfer, this is done by typing: $recon-all -subjid NAME -i PATH2MRI Here NAME refers to what you want the folder in $SUBJECT DIR to be named, and it will store all the output related to the MRI. PATH2MRI refers to the complete path to a nifti file or a single DICOM file in a serie. The next step is to type : $recon-all -subjid NAME -all The flag -all will initialize a complete FreeSurfer process. Lars Magnus Valnes (UiO) FreeSurfer March 4, / 20
23 Running FreeSurfer The first step is to input the MRIs to FreeSurfer, this is done by typing: $recon-all -subjid NAME -i PATH2MRI Here NAME refers to what you want the folder in $SUBJECT DIR to be named, and it will store all the output related to the MRI. PATH2MRI refers to the complete path to a nifti file or a single DICOM file in a serie. The next step is to type : $recon-all -subjid NAME -all The flag -all will initialize a complete FreeSurfer process. The process is stepwise and each step is described here. Lars Magnus Valnes (UiO) FreeSurfer March 4, / 20
24 Running FreeSurfer The first step is to input the MRIs to FreeSurfer, this is done by typing: $recon-all -subjid NAME -i PATH2MRI Here NAME refers to what you want the folder in $SUBJECT DIR to be named, and it will store all the output related to the MRI. PATH2MRI refers to the complete path to a nifti file or a single DICOM file in a serie. The next step is to type : $recon-all -subjid NAME -all The flag -all will initialize a complete FreeSurfer process. The process is stepwise and each step is described here. For more through details, I recommend reading the relate articles found here. Lars Magnus Valnes (UiO) FreeSurfer March 4, / 20
25 Output Structure in FreeSurfer The output will be written to folders in $SUBJECTS DIR/subjid, and we can look at the folders by typing : Lars Magnus Valnes (UiO) FreeSurfer March 4, / 20
26 Output Structure in FreeSurfer The output will be written to folders in $SUBJECTS DIR/subjid, and we can look at the folders by typing : $recon-all -subjid name -i path to dicom $ls $SUBJECTS DIR/name Lars Magnus Valnes (UiO) FreeSurfer March 4, / 20
27 File Formats in FreeSurfer FreeSurfer will generate many different types of files, thus we will have a short introduction to a selected few. Lars Magnus Valnes (UiO) FreeSurfer March 4, / 20
28 File Formats in FreeSurfer FreeSurfer will generate many different types of files, thus we will have a short introduction to a selected few. The extension.mgh is volume of voxels and a compressed.mgh file has the the extension.mgz. Lars Magnus Valnes (UiO) FreeSurfer March 4, / 20
29 File Formats in FreeSurfer FreeSurfer will generate many different types of files, thus we will have a short introduction to a selected few. The extension.mgh is volume of voxels and a compressed.mgh file has the the extension.mgz. Surface files, which are 3D triangulated binary surface files. Lars Magnus Valnes (UiO) FreeSurfer March 4, / 20
30 File Formats in FreeSurfer FreeSurfer will generate many different types of files, thus we will have a short introduction to a selected few. The extension.mgh is volume of voxels and a compressed.mgh file has the the extension.mgz. Surface files, which are 3D triangulated binary surface files. Label are text files with vertices and corresponding values ( integer or string), Label file Lars Magnus Valnes (UiO) FreeSurfer March 4, / 20
31 File Formats in FreeSurfer FreeSurfer will generate many different types of files, thus we will have a short introduction to a selected few. The extension.mgh is volume of voxels and a compressed.mgh file has the the extension.mgz. Surface files, which are 3D triangulated binary surface files. Label are text files with vertices and corresponding values ( integer or string), Label file Annotation files contains a collection of labels, and also includes a colour table Lars Magnus Valnes (UiO) FreeSurfer March 4, / 20
32 File Formats in FreeSurfer FreeSurfer will generate many different types of files, thus we will have a short introduction to a selected few. The extension.mgh is volume of voxels and a compressed.mgh file has the the extension.mgz. Surface files, which are 3D triangulated binary surface files. Label are text files with vertices and corresponding values ( integer or string), Label file Annotation files contains a collection of labels, and also includes a colour table Atlas contains probabilistic information estimated to label neuroanatomy each location on a cortical surface model. Lars Magnus Valnes (UiO) FreeSurfer March 4, / 20
33 File Formats in FreeSurfer FreeSurfer will generate many different types of files, thus we will have a short introduction to a selected few. The extension.mgh is volume of voxels and a compressed.mgh file has the the extension.mgz. Surface files, which are 3D triangulated binary surface files. Label are text files with vertices and corresponding values ( integer or string), Label file Annotation files contains a collection of labels, and also includes a colour table Atlas contains probabilistic information estimated to label neuroanatomy each location on a cortical surface model. Template used to analyse longitudinal volumes. Lars Magnus Valnes (UiO) FreeSurfer March 4, / 20
34 Surface Files For this presentation we will focus on surface files, and there are different types : Lars Magnus Valnes (UiO) FreeSurfer March 4, / 20
35 Surface Files For this presentation we will focus on surface files, and there are different types :?h.pial surface displays gyri and sulci, the sulci is barely visible. Lars Magnus Valnes (UiO) FreeSurfer March 4, / 20
36 Surface Files For this presentation we will focus on surface files, and there are different types :?h.pial surface displays gyri and sulci, the sulci is barely visible.?h.white surface displays boundary between white and grey matter. Lars Magnus Valnes (UiO) FreeSurfer March 4, / 20
37 Surface Files For this presentation we will focus on surface files, and there are different types :?h.pial surface displays gyri and sulci, the sulci is barely visible.?h.white surface displays boundary between white and grey matter.?h.inflated surface shows fully the sulci. Lars Magnus Valnes (UiO) FreeSurfer March 4, / 20
38 Surface Files For this presentation we will focus on surface files, and there are different types :?h.pial surface displays gyri and sulci, the sulci is barely visible.?h.white surface displays boundary between white and grey matter.?h.inflated surface shows fully the sulci. Lars Magnus Valnes (UiO) FreeSurfer March 4, / 20
39 Coordinate Systems FreeSurfer works with multiple coordinate systems, and we will look at most of them. Lars Magnus Valnes (UiO) FreeSurfer March 4, / 20
40 Coordinate Systems FreeSurfer works with multiple coordinate systems, and we will look at most of them. Scanner-space, often LPS (Left Posterior Superior) Lars Magnus Valnes (UiO) FreeSurfer March 4, / 20
41 Coordinate Systems FreeSurfer works with multiple coordinate systems, and we will look at most of them. Scanner-space, often LPS (Left Posterior Superior) Voxel coordinates, (256,256,256) Lars Magnus Valnes (UiO) FreeSurfer March 4, / 20
42 Coordinate Systems FreeSurfer works with multiple coordinate systems, and we will look at most of them. Scanner-space, often LPS (Left Posterior Superior) Voxel coordinates, (256,256,256) Scanner RAS-coordinates, stands for Right Anterior Superior Lars Magnus Valnes (UiO) FreeSurfer March 4, / 20
43 Coordinate Systems FreeSurfer works with multiple coordinate systems, and we will look at most of them. Scanner-space, often LPS (Left Posterior Superior) Voxel coordinates, (256,256,256) Scanner RAS-coordinates, stands for Right Anterior Superior TkReg-RAS, the coordinate system for tksurfer and surfaces. Lars Magnus Valnes (UiO) FreeSurfer March 4, / 20
44 Coordinate Systems FreeSurfer works with multiple coordinate systems, and we will look at most of them. Scanner-space, often LPS (Left Posterior Superior) Voxel coordinates, (256,256,256) Scanner RAS-coordinates, stands for Right Anterior Superior TkReg-RAS, the coordinate system for tksurfer and surfaces. More details are found here. Lars Magnus Valnes (UiO) FreeSurfer March 4, / 20
45 Freeview Freeview is graphic user interface for FreeSurfer, and can be opened by typing : $ freeview. Lars Magnus Valnes (UiO) FreeSurfer March 4, / 20
46 Freeview Freeview is graphic user interface for FreeSurfer, and can be opened by typing : $ freeview. Lars Magnus Valnes (UiO) FreeSurfer March 4, / 20
47 Freeview Freeview is graphic user interface for FreeSurfer, and can be opened by typing : $ freeview. We can also add flags with more specifications: Lars Magnus Valnes (UiO) FreeSurfer March 4, / 20
48 Freeview Freeview is graphic user interface for FreeSurfer, and can be opened by typing : $ freeview. We can also add flags with more specifications: -v $SUBJECTS DIR/bert/mri/aseg.mgz:colormap=lut:opacity=0.2 -f $SUBJECTS DIR/bert/surf/rh.white:edgecolor=blue -f $SUBJECTS DIR/bert/surf/lh.white:annot=aparc.annot:name=pial aparc:visible=0 Lars Magnus Valnes (UiO) FreeSurfer March 4, / 20
49 Freeview Working in Freeview When working with surface files, it can be Lars Magnus Valnes (UiO) FreeSurfer March 4, / 20
50 Freeview Working in Freeview When working with surface files, it can be Overlay, load a thickness file to see the thickness of the surface. Lars Magnus Valnes (UiO) FreeSurfer March 4, / 20
51 Freeview Working in Freeview When working with surface files, it can be Overlay, load a thickness file to see the thickness of the surface. Annotation, will display a collection of labels on a surface. Lars Magnus Valnes (UiO) FreeSurfer March 4, / 20
52 Freeview Working in Freeview When working with surface files, it can be Overlay, load a thickness file to see the thickness of the surface. Annotation, will display a collection of labels on a surface. Curvature, shows the curvature of the surface. Lars Magnus Valnes (UiO) FreeSurfer March 4, / 20
53 Freeview Working in Freeview When working with surface files, it can be Overlay, load a thickness file to see the thickness of the surface. Annotation, will display a collection of labels on a surface. Curvature, shows the curvature of the surface. Label, will highlight a specific part of the surface. Lars Magnus Valnes (UiO) FreeSurfer March 4, / 20
54 Mesh Extraction Introduction Mesh extraction is to obtain a 3D triangulated surface file from Freesurfer and we will look at : Lars Magnus Valnes (UiO) FreeSurfer March 4, / 20
55 Mesh Extraction Introduction Mesh extraction is to obtain a 3D triangulated surface file from Freesurfer and we will look at : Scripts from brainder.org. Lars Magnus Valnes (UiO) FreeSurfer March 4, / 20
56 Mesh Extraction Introduction Mesh extraction is to obtain a 3D triangulated surface file from Freesurfer and we will look at : Scripts from brainder.org. FreeSurfer commands Lars Magnus Valnes (UiO) FreeSurfer March 4, / 20
57 Mesh Extraction Command for extraction of a 3D triangulated surface file. If we have a 3D triangulated surface file, we can simply type : $mkdir $SUBJECTS DIR/bert/asc $mris convert $SUBJECTS DIR/bert/surf/lh.pial $SUBJECTS DIR/bert/asc/lh pial.asc Lars Magnus Valnes (UiO) FreeSurfer March 4, / 20
58 Mesh Extraction Brainder scripts Brainder.org is a sharing website with application towards FreeSurfer. Lars Magnus Valnes (UiO) FreeSurfer March 4, / 20
59 Mesh Extraction Brainder scripts Brainder.org is a sharing website with application towards FreeSurfer. Generating the surfaces for subcortical structures, aseg2srf.sh Lars Magnus Valnes (UiO) FreeSurfer March 4, / 20
60 Mesh Extraction Brainder scripts Brainder.org is a sharing website with application towards FreeSurfer. Generating the surfaces for subcortical structures, aseg2srf.sh Importing FreeSurfer cortical meshes into Blender, srf2obj.gawk Lars Magnus Valnes (UiO) FreeSurfer March 4, / 20
61 Mesh Extraction The Script aseg2srf.sh Lars Magnus Valnes (UiO) FreeSurfer March 4, / 20
62 Mesh Extraction The Script aseg2srf.sh Obtains the mesh from a volume of voxels. Lars Magnus Valnes (UiO) FreeSurfer March 4, / 20
63 Mesh Extraction The Script aseg2srf.sh Obtains the mesh from a volume of voxels. Can have topological defects. Lars Magnus Valnes (UiO) FreeSurfer March 4, / 20
64 Mesh Extraction The Script aseg2srf.sh Obtains the mesh from a volume of voxels. Can have topological defects. aseg2srf.sh Lars Magnus Valnes (UiO) FreeSurfer March 4, / 20
65 Surface Generation Commands for Skull Surface We can also obtain surfaces by adding optional inputs to FreeSurfer commands. $mri watershed -usesras -surf $SUBJECT DIR/bert/surf/outer $SUBJECT DIR/bert/mri/orig nu.mgz $SUBJECT DIR/bert/trash/trash.mgz Lars Magnus Valnes (UiO) FreeSurfer March 4, / 20
66 Surface Generation Commands for Skull Surface We can also obtain surfaces by adding optional inputs to FreeSurfer commands. $mri watershed -usesras -surf $SUBJECT DIR/bert/surf/outer $SUBJECT DIR/bert/mri/orig nu.mgz $SUBJECT DIR/bert/trash/trash.mgz This command will generate four surfaces : Inner skull Lars Magnus Valnes (UiO) FreeSurfer March 4, / 20
67 Surface Generation Commands for Skull Surface We can also obtain surfaces by adding optional inputs to FreeSurfer commands. $mri watershed -usesras -surf $SUBJECT DIR/bert/surf/outer $SUBJECT DIR/bert/mri/orig nu.mgz $SUBJECT DIR/bert/trash/trash.mgz This command will generate four surfaces : Inner skull Outer skull Lars Magnus Valnes (UiO) FreeSurfer March 4, / 20
68 Surface Generation Commands for Skull Surface We can also obtain surfaces by adding optional inputs to FreeSurfer commands. $mri watershed -usesras -surf $SUBJECT DIR/bert/surf/outer $SUBJECT DIR/bert/mri/orig nu.mgz $SUBJECT DIR/bert/trash/trash.mgz This command will generate four surfaces : Inner skull Outer skull Outer skin Lars Magnus Valnes (UiO) FreeSurfer March 4, / 20
69 Surface Generation Commands for Skull Surface We can also obtain surfaces by adding optional inputs to FreeSurfer commands. $mri watershed -usesras -surf $SUBJECT DIR/bert/surf/outer $SUBJECT DIR/bert/mri/orig nu.mgz $SUBJECT DIR/bert/trash/trash.mgz This command will generate four surfaces : Inner skull Outer skull Outer skin Brain surface Lars Magnus Valnes (UiO) FreeSurfer March 4, / 20
70 Mesh Extraction Inner and Outer Skull Lars Magnus Valnes (UiO) FreeSurfer March 4, / 20
71 Mesh Extraction Surf2Mesh Lars Magnus Valnes (UiO) FreeSurfer March 4, / 20
72 Mesh Extraction Surf2Mesh A set of scripts to create a mesh from a.asc file can be seen here. Lars Magnus Valnes (UiO) FreeSurfer March 4, / 20
73 Mesh Extraction Surf2Mesh A set of scripts to create a mesh from a.asc file can be seen here. Contains.asc to.off/.stl conversion, will preferably become obsolete. Lars Magnus Valnes (UiO) FreeSurfer March 4, / 20
74 Mesh Extraction Surf2Mesh A set of scripts to create a mesh from a.asc file can be seen here. Contains.asc to.off/.stl conversion, will preferably become obsolete. Also there are some scripts to simplify the mesh creation. Lars Magnus Valnes (UiO) FreeSurfer March 4, / 20
75 Mesh Extraction Surf2Mesh A set of scripts to create a mesh from a.asc file can be seen here. Contains.asc to.off/.stl conversion, will preferably become obsolete. Also there are some scripts to simplify the mesh creation. Extmesh utility.py Lars Magnus Valnes (UiO) FreeSurfer March 4, / 20
76 Mesh Extraction Viewing Mesh in Paraview Lars Magnus Valnes (UiO) FreeSurfer March 4, / 20
77 Ending Future Lars Magnus Valnes (UiO) FreeSurfer March 4, / 20
78 Ending Future Python module Nibabel. Lars Magnus Valnes (UiO) FreeSurfer March 4, / 20
79 Ending Future Python module Nibabel. Register commands. Lars Magnus Valnes (UiO) FreeSurfer March 4, / 20
80 Ending Future Python module Nibabel. Register commands. Accurately marking subdomains of extracted mesh. Lars Magnus Valnes (UiO) FreeSurfer March 4, / 20
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