FreeSurfer Reader-3766

Surgical Planning Laboratoryhttp://www.slicer.org-1-

Brigham and Women’s Hospital

Slicer Tutorial 6 Module: vtkFreeSurferReaders

Sonia Pujol, Ph.D.

Randy Gollub, M.D., Ph.D.



AcknowledgmentsNational Alliance for Medical Image ComputingNIH U54EB005149

Neuroimage Analysis Center NIH P41RR013218

Center for Functional Neuroimaging TechnologiesNIH P41RR14075

Morphometry Biomedical Informatics Research Network NIH U24 RRO21382

Surgical Planning LaboratoryThanks to Nicole Aucoin



Disclaimer

It is the responsibility of the user of 3DSlicer

and FreeSurfer to comply with both the terms

of the licenses and with the applicable laws,

regulations and rules.



Materials Needed

• Slicer 2.5MGHhttp://www.na-mic.org/Wiki/index.php/Slicer:Slicer2.5MGH_Getting_Started

• Free Surfer Sample Data: FreesurferSubjects.ziphttp://www.na-mic.org/Wiki/index.php/Slicer:Workshops:User_Training_101



Goal of this tutorial

Guide you step-by-step through the process of loading and viewing FreeSurfer segmentation, surface reconstruction and parcellation results within Slicer.



Prerequisites

This tutorial assumes a working

knowledge of how to use

FreeSurfer to generate the

segmentation and surface files.

Tutorial materials for FreeSurfer

are available at

https://surfer.nmr.mgh.harvard.edu/fswiki

https://surfer.nmr.mgh.harvard.edu/docs/ftp/pub/docs/fsTutorial/



Prerequisites

This tutorial assumes a basic

knowledge of how to use

3DSlicer.

Slicer Training 1: Loading

and Viewing Data

Slicer Training 7: Saving Data

http://www.namic.org/Wiki/index.php/

Slicer:Workshops:User_Training_101



vtkFreeSurferReaders Module



Loading FreeSurfer Data

Slicer can load

• Brain Volumes …………………….

• ASEG Volumes ………………………

• Surfaces…………………………………

• Overlays ………………………………….



•Part 1: Loading FreeSurfer Volumes

•Part 2: Overlay Brain and Segmentation

•Part 3: Building 3D Models

•Part 4: Loading Surfaces

•Part 5: Group Statistics

Overview of Training 6




Select the Menu Modules in the Main Panel

Select the category IO and the module vtkFreeSurferReaders




The vtkFreeSurferReaders module appears in the Main Panel of Slicer.

The Volumes tab comes up by default.



Loading a Brain file

Brain.mgz

Skull Stripping and Noise Filtering

Watershed algorithm

Intensity corrected

T1 volumeFreeSurfer Pipeline




Select the Tab Volumes in the FreeSurfer Module

Click on Browse and select the subject bert

Click on the mri folder to access the brain volume.



Loading a Brain fileSelect the file brain.mgz

Select the data type GrayScale

Click Apply




The volume Brain.mgz appears in the Viewer.




Click on the V buttons in the Axial, Sagittal and Coronal views.




The three anatomical slices appear in the 3D Viewer.



Loading an ASEG file

Aseg.mgz

Segmentation

Subcortical processing

Intensity corrected

T1 volumeFreeSurfer Pipeline




Select the Tab Volumes in the FreeSurfer Module.

Click on Browse and select the subject bert

Click on the mri folder to access the aseg volume.



Loading an ASEG fileSelect the file aseg.mgz

Select the data type Label Map

Click on Apply




The labels are superimposed on the gray level brain images.

The volume aseg.mgz appears in the Viewer.



Determining label numbers in an ASEG file# ColHeaders Index SegId NVoxels Volume_mm3 SegName Mean StdDev Min Max Range1 1 0 0.0 Left-Cerebral-Exterior 0.0000 0.0000 0.0000 0.0000 0.00002 2 245171 245171.0 Left-Cerebral-White-Matter 121.7886 8.0072 40.0000 186.0000 146.00003 3 287069 287069.0 Left-Cerebral-Cortex 91.3494 13.8505 31.0000 220.0000 189.00004 4 6876 6876.0 Left-Lateral-Ventricle 48.2126 14.3628 25.0000 106.0000 81.00005 5 200 200.0 Left-Inf-Lat-Vent 67.3513 10.8024 35.0000 102.0000 67.00006 6 0 0.0 Left-Cerebellum-Exterior 0.0000 0.0000 0.0000 0.0000 0.00007 7 10514 10514.0 Left-Cerebellum-White-Matter 120.4405 8.5863 43.0000 134.0000 91.00008 8 66561 66561.0 Left-Cerebellum-Cortex 98.8117 14.1726 32.0000 211.0000 179.00009 9 0 0.0 Left-Thalamus 0.0000 0.0000 0.0000 0.0000 0.000010 10 9887 9887.0 Left-Thalamus-Proper 113.5839 10.3047 45.0000 133.0000 88.000011 11 3819 3819.0 Left-Caudate 102.9627 12.1416 62.0000 132.0000 70.000012 12 6755 6755.0 Left-Putamen 110.0479 7.4787 76.0000 132.0000 56.000013 13 2229 2229.0 Left-Pallidum 122.5797 4.2841 105.0000 134.0000 29.000014 14 793 793.0 3rd-Ventricle 54.2582 15.3296 28.0000 93.0000 65.000015 15 1819 1819.0 4th-Ventricle 51.8305 15.5400 27.0000 108.0000 81.000016 16 26616 26616.0 Brain-Stem 113.1949 12.7048 39.0000 136.0000 97.000017 17 4489 4489.0 Left-Hippocampus 96.0929 8.6315 56.0000 122.0000 66.000018 18 1869 1869.0 Left-Amygdala 94.8671 8.2028 61.0000 118.0000 57.000019 19 0 0.0 Left-Insula 0.0000 0.0000 0.0000 0.0000 0.000020 20 0 0.0 Left-Operculum 0.0000 0.0000 0.0000 0.0000 0.000021 21 0 0.0 Line-1 0.0000 0.0000 0.0000 0.0000 0.000022 22 0 0.0 Line-2 0.0000 0.0000 0.0000 0.0000 0.000023 23 0 0.0 Line-3 0.0000 0.0000 0.0000 0.0000 0.000024 24 1611 1611.0 CSF 59.9684 15.4368 30.0000 107.0000 77.000025 25 0 0.0 Left-Lesion 0.0000 0.0000 0.0000 0.0000 0.000026 26 733 733.0 Left-Accumbens-area 97.8124 6.7471 67.0000 121.0000 54.000027 27 0 0.0 Left-Substancia-Nigra 0.0000 0.0000 0.0000 0.0000 0.000028 28 3957 3957.0 Left-VentralDC 117.4001 10.5813 47.0000 135.0000 88.000029 29 0 0.0 Left-undetermined 0.0000 0.0000 0.0000 0.0000 0.000030 30 56 56.0 Left-vessel 81.5250 7.9485 62.0000 97.0000 35.0000

The file aseg.stats gives the list of the available segmented structures in the dataset.

Example of the first 30 structures.



# ColHeaders Index SegId NVoxels Volume_mm3 SegName Mean StdDev Min Max Range1 1 0 0.0 Left-Cerebral-Exterior 0.0000 0.0000 0.0000 0.0000 0.00002 2 245171 245171.0 Left-Cerebral-White-Matter 121.7886 8.0072 40.0000 186.0000 146.00003 3 287069 287069.0 Left-Cerebral-Cortex 91.3494 13.8505 31.0000 220.0000 189.00004 4 6876 6876.0 Left-Lateral-Ventricle 48.2126 14.3628 25.0000 106.0000 81.00005 5 200 200.0 Left-Inf-Lat-Vent 67.3513 10.8024 35.0000 102.0000 67.00006 6 0 0.0 Left-Cerebellum-Exterior 0.0000 0.0000 0.0000 0.0000 0.00007 7 10514 10514.0 Left-Cerebellum-White-Matter 120.4405 8.5863 43.0000 134.0000 91.00008 8 66561 66561.0 Left-Cerebellum-Cortex 98.8117 14.1726 32.0000 211.0000 179.00009 9 0 0.0 Left-Thalamus 0.0000 0.0000 0.0000 0.0000 0.000010 10 9887 9887.0 Left-Thalamus-Proper 113.5839 10.3047 45.0000 133.0000 88.000011 11 3819 3819.0 Left-Caudate 102.9627 12.1416 62.0000 132.0000 70.000012 12 6755 6755.0 Left-Putamen 110.0479 7.4787 76.0000 132.0000 56.000013 13 2229 2229.0 Left-Pallidum 122.5797 4.2841 105.0000 134.0000 29.000014 14 793 793.0 3rd-Ventricle 54.2582 15.3296 28.0000 93.0000 65.000015 15 1819 1819.0 4th-Ventricle 51.8305 15.5400 27.0000 108.0000 81.000016 16 26616 26616.0 Brain-Stem 113.1949 12.7048 39.0000 136.0000 97.000017 17 4489 4489.0 Left-Hippocampus 96.0929 8.6315 56.0000 122.0000 66.000018 18 1869 1869.0 Left-Amygdala 94.8671 8.2028 61.0000 118.0000 57.000019 19 0 0.0 Left-Insula 0.0000 0.0000 0.0000 0.0000 0.000020 20 0 0.0 Left-Operculum 0.0000 0.0000 0.0000 0.0000 0.000021 21 0 0.0 Line-1 0.0000 0.0000 0.0000 0.0000 0.000022 22 0 0.0 Line-2 0.0000 0.0000 0.0000 0.0000 0.000023 23 0 0.0 Line-3 0.0000 0.0000 0.0000 0.0000 0.000024 24 1611 1611.0 CSF 59.9684 15.4368 30.0000 107.0000 77.000025 25 0 0.0 Left-Lesion 0.0000 0.0000 0.0000 0.0000 0.000026 26 733 733.0 Left-Accumbens-area 97.8124 6.7471 67.0000 121.0000 54.000027 27 0 0.0 Left-Substancia-Nigra 0.0000 0.0000 0.0000 0.0000 0.000028 28 3957 3957.0 Left-VentralDC 117.4001 10.5813 47.0000 135.0000 88.000029 29 0 0.0 Left-undetermined 0.0000 0.0000 0.0000 0.0000 0.000030 30 56 56.0 Left-vessel 81.5250 7.9485 62.0000 97.0000 35.0000

The label #10 represents the Left-Thalamus Proper.

The corresponding segmented volume is available in the current dataset.

Determining label numbers in an ASEG file



# ColHeaders Index SegId NVoxels Volume_mm3 SegName Mean StdDev Min Max Range1 1 0 0.0 Left-Cerebral-Exterior 0.0000 0.0000 0.0000 0.0000 0.00002 2 245171 245171.0 Left-Cerebral-White-Matter 121.7886 8.0072 40.0000 186.0000 146.00003 3 287069 287069.0 Left-Cerebral-Cortex 91.3494 13.8505 31.0000 220.0000 189.00004 4 6876 6876.0 Left-Lateral-Ventricle 48.2126 14.3628 25.0000 106.0000 81.00005 5 200 200.0 Left-Inf-Lat-Vent 67.3513 10.8024 35.0000 102.0000 67.00006 6 0 0.0 Left-Cerebellum-Exterior 0.0000 0.0000 0.0000 0.0000 0.00007 7 10514 10514.0 Left-Cerebellum-White-Matter 120.4405 8.5863 43.0000 134.0000 91.00008 8 66561 66561.0 Left-Cerebellum-Cortex 98.8117 14.1726 32.0000 211.0000 179.00009 9 0 0.0 Left-Thalamus 0.0000 0.0000 0.0000 0.0000 0.000010 10 9887 9887.0 Left-Thalamus-Proper 113.5839 10.3047 45.0000 133.0000 88.000011 11 3819 3819.0 Left-Caudate 102.9627 12.1416 62.0000 132.0000 70.000012 12 6755 6755.0 Left-Putamen 110.0479 7.4787 76.0000 132.0000 56.000013 13 2229 2229.0 Left-Pallidum 122.5797 4.2841 105.0000 134.0000 29.000014 14 793 793.0 3rd-Ventricle 54.2582 15.3296 28.0000 93.0000 65.000015 15 1819 1819.0 4th-Ventricle 51.8305 15.5400 27.0000 108.0000 81.000016 16 26616 26616.0 Brain-Stem 113.1949 12.7048 39.0000 136.0000 97.000017 17 4489 4489.0 Left-Hippocampus 96.0929 8.6315 56.0000 122.0000 66.000018 18 1869 1869.0 Left-Amygdala 94.8671 8.2028 61.0000 118.0000 57.000019 19 0 0.0 Left-Insula 0.0000 0.0000 0.0000 0.0000 0.000020 20 0 0.0 Left-Operculum 0.0000 0.0000 0.0000 0.0000 0.000021 21 0 0.0 Line-1 0.0000 0.0000 0.0000 0.0000 0.000022 22 0 0.0 Line-2 0.0000 0.0000 0.0000 0.0000 0.000023 23 0 0.0 Line-3 0.0000 0.0000 0.0000 0.0000 0.000024 24 1611 1611.0 CSF 59.9684 15.4368 30.0000 107.0000 77.000025 25 0 0.0 Left-Lesion 0.0000 0.0000 0.0000 0.0000 0.000026 26 733 733.0 Left-Accumbens-area 97.8124 6.7471 67.0000 121.0000 54.000027 27 0 0.0 Left-Substancia-Nigra 0.0000 0.0000 0.0000 0.0000 0.000028 28 3957 3957.0 Left-VentralDC 117.4001 10.5813 47.0000 135.0000 88.000029 29 0 0.0 Left-undetermined 0.0000 0.0000 0.0000 0.0000 0.000030 30 56 56.0 Left-vessel 81.5250 7.9485 62.0000 97.0000 35.0000

The label #19 representing the Left-Insula.

The corresponding segmented volume is not available in the current dataset.

Determining label numbers in an ASEG file



Click on the button Bg (Background) and select the volume aseg in the Axial view.

Overlay Brain and Segmentation




Move the mouse over the labels in the Axial view.




The names of the labels appear in the window.




Find the labels corresponding to the Left Thalamus Proper, Left Caudate and Left Putamen in the three anatomical views.




Left Thalamus Proper = 10




Left Putamen = 12




Left Caudate = 11




Select View3D in the MainMenu




Drag right mouse button down in the 3D Viewer to zoom in.




The Viewer displays a zoom view of the brain and aseg slices superimposed.

Drag right mouse button up in the Viewer to zoom out.



Building a single Model

Select the module ModelMaker in the MainMenu

Select the panel Create

Select the Volume aseg and click on the button Label




Slicer displays the Color Map corresponding to the structures that FreeSurfer can segment.




Move the mouse over the table and select the label of the right hippocampus (label 53).




The label of the right hippocampus appears in the Create panel.

Click on Create to build the 3D model.




The 3D model of the right hippocampus appears in the Viewer.

Switch to the view 3D, and drag right mouse button down in the Viewer to zoom in.




Slicer displays a zoom view of the right hippocampus.



Building 3D Models

Select the module ModelMaker in the MainMenu

Select the panel

Create Multiple



Building 3D Models

Select the Volume aseg and click on the button Starting Label

The Panel Create Multiple provides the interface to build a set of continuous models from the values in the interval

[Starting Label, Ending Label]



Building 3D Models

Click on the label corresponding to the Left Thalamus Proper (Label 10).



Building 3D Models

Click on the button Ending Label

The value and the color of the selected label appear in the panel.



Building 3D Models

Click on the label corresponding to the Left Pallidum (Label 13).



Building 3D Models

Click on Create all to build the 3D models of the selected labels.

Slicer reconstructs the 3D models from the labels 10,11,12 and 13.



Building 3D Models

The 3D models of the selected structures appear inside the Viewer.



Building 3D Models

Left click and move the mouse to orient the models in the Viewer



Building 3D Models

Click in the module Models in the Main Menu and select the panel Display.

The list of models appears in the panel.

Deselect the models of the Left Putamen and Left Caudate.



Building 3D Models

Slicer displays the left Thalamus Proper, left Pallidum and right Hippocampus in the Viewer.



Building 3D Models

Click on Show None to make all the models disappear from the Scene.



Loading Surfaces

Select the panel Models in the vtkFreeSurferReaders module.

Click on Browse and select the surface lh.white in the directory subjects/bert/surf



Loading Surfaces

Click Apply to load the surface in Slicer.

The name of the surface selected appears in the Models panel.



Loading Surface

The surface of the white matter of the left hemisphere appears in the Viewer.



Parcellation Visualization

In the panel Models click on aparc to select the parcellation map of the model lh.white

Click on Apply to load the overlay.




Slicer displays the parcellation results overlaid on the white matter surface in the Viewer.

Switch to 3D view in the main menu and zoom in the model.




Cortical parcellation of the white matter surface in the left hemisphere.



Group Statistics•After completion of surface reconstruction for all subjects in a study, FreeSurfer can perform group averaging and statistical inference of the cortical surface measurements such as thickness.

•The observed data is a set of cortical surface measurements at each vertex for each subject in the group.

•The process fits a General Linear Model at each vertex to summarize the data from all the subjects.

•The group analysis results in a statistical parametric map that can be loaded into Slicer for visualisation as an overlay on the average surface.



Group Statistics

Statistical Parametric Map

Average Subject creation

General Linear Modeling



Group Statistics - example

Statistical Parametric Map

sigt_Age_dossthickness-100lh.w

Average Subject creation

lh.pial_avg

For my cohort of x sujects, does cortical thickness vary with age?

General Linear Modeling

y_doss_thickness-100lh.fsgd



Group Statistics

Select the Tab Models in the vtkFreeSurferReaders module.

Click on Browse and select the surface lh.pial_avg in the directory subjects/average/surf



Group Statistics

Select the Tab Display in the vtkFreeSurferReaders module.

Click on Browse and select the overlay subjects/stats/sigt_Age_doss-thickness-100lh.w

Click on Load Scalar File.



Group Statistics

Slicer displays the statistical map as an overlay superimposed on the average surface.

Move the model with the mouse to update the Viewer display.



Group Statistics

Select the Panel Plot in the vtkFreeSurferReaders module.

Click on Browse and select the file y_doss-thickness-100lh.fsgd in the directory subjects/stats.



Group Statistics

Select the Active Model lh.pial_avg in the list of models.

Click on Apply to load the Group Statistics results.



Group Statistics

Slicer displays statistical distribution of the cortical thickness of the left hemisphere parameterized by the age of the population.



Group Statistics

Select the Mode subject in the Group Statistics Window.



Group Statistics

Slicer displays the subjects included in the Statistical Analysis.

Move the mouse over the subjects table and select the subject #108.



Group Statistics

A red circle shows the position of the subject #108 in the analysis.



Group Statistics

The Configure Classes menu displays the visualization options of the population.



Group Statistics

Select the pattern diamond and the color black for the male subjects.

Select the pattern circle and the color purple for the female subjects.



Group Statistics

Slicer updates the interface with the new configuration parameters.



To generate a plot for a particular vertex, select a point by clicking on the parametric map at that vertex on the 3D model in the Viewer

Group Statistics



Slicer updates the thickness results with the values corresponding to the selected vertex.

Group Statistics



Conclusion

• 3D visualization of brain segmentedsurfaces, parcellation maps andstatistical results from FreeSurfer

• Intuitive graphical user interface to interact with the data

• Open-Source environment

FreeSurfer Reader-3766

Health & Medicine

Transcript of FreeSurfer Reader-3766