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You can explore data in a number of different viewing fields, and orientations. To see all orientations at once, including the 3D representation, choose from the toolbar on the top either 2x2 {{attachment:2x2icon.gif}}, 1&3 {{attachment:1x3icon.gif}}, 1&3 horizontal {{attachment:1x3horizicon.gif}}. To have one orientation as full screen, choose the 1x1 option {{attachment:1x1icon.gif}}. To the right of these buttons are the buttons with which you can change the orientation: saggital {{attachment:saggital.gif}}, coronal {{attachment:coronal.gif}}, axial {{attachment:axial.gif}}, and 3D {{attachment:3D.gif}}. You can explore data in a number of different viewing fields, and orientations. To see all orientations at once, including the 3D representation, choose from the toolbar on the top either 2x2 {{attachment:layout_2x2.gif}}, 1&3 {{attachment:layout_1n3.gif}}, 1&3 horizontal {{attachment:layout_1n3_h.gif}}. To have one orientation as full screen, choose the 1x1 option {{attachment:layout_1x1.gif}}. To the right of these buttons are the buttons with which you can change the orientation: saggital {{attachment:view_sagittal.gif}}, coronal {{attachment:view_coronal.gif}}, axial {{attachment:view_axial.gif}}, and 3D {{attachment:view_3d.gif}}.
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In the top, left corner of the window, directly beneath the File and Edit menus you can switch between '''Navigate''' {{attachment:NavigatorIcon.gif}} and '''Voxel Edit''' {{attachment:VoxelEditIcon.gif}} modes. While in Navigate mode, you can use the mouse to move the red crosshairs and navigate through the data. Click to Voxel Edit mode, a drawing toolbox appears, and you can draw upon the volume. In the lefthand control panel, you can change Color Maps, adjust the opacity (useful when working with multiple volumes in the same window), and adjust the contrast (Window, Level, Min and Max sliding bars). In the top, left corner of the window, directly beneath the File and Edit menus you can switch between '''Navigate''' {{attachment:navigate.gif}} and '''Voxel Edit''' {{attachment:voxel_edit.gif}} modes. While in Navigate mode, you can use the mouse to move the red crosshairs and navigate through the data. Click to Voxel Edit mode, a drawing toolbox appears, and you can draw upon the volume. In the lefthand control panel, you can change Color Maps, adjust the opacity (useful when working with multiple volumes in the same window), and adjust the contrast (Window, Level, Min and Max sliding bars).
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To save data and volumes, go to '''File'''>'''Save Volume''' or click this icon {{attachment:savevolumeicon.gif}}. If it was a new volume, never before saved, it will ask you to again enter the desired volume name. Do so, and click OK. If it was a previously saved volume that you made changes to, it will continue saving under that volume name. There is a blue activity bar in the bottom right corner of Freeview. This shows the progress of loading and/or saving volumes. Be sure to wait until it is done saving before exiting Freeview. You can also check in the terminal window for a message stating that your volume has saved successfully. Note: you can continue working and making changes while it is saving, but again, be sure to save the most updated version before exiting! To save data and volumes, go to '''File'''>'''Save Volume''' or click the save icon {{attachment:savevolumeicon.gif}}. If it was a new volume, never before saved, it will ask you to again enter the desired volume name. Do so, and click OK. If it was a previously saved volume that you made changes to, it will continue saving under that volume name. There is a blue activity bar in the bottom right corner of Freeview. This shows the progress of loading and/or saving volumes. Be sure to wait until it is done saving before exiting Freeview. You can also check in the terminal window for a message stating that your volume has saved successfully. Note: you can continue working and making changes while it is saving, but again, be sure to save the most updated version before exiting!

Up to FreeviewGuide

Back to FreeviewGeneralUsage

Continue to FreeviewInterface

Quick Start

Freeview is started by invoking it from the command line. The user must first source the developmental (updated regularly) version of Freesurfer by opening a terminal window and typing (or copy-pasting) this command:

source  /usr/local/freesurfer/nmr-dev-env

The user must next navigate to the directory in which the volume is saved in order to open it. Example:

cd /autofs/space/rainbow_002/users/hires/FHS19_ec_amyg_032808/mri/flash

Be sure to type the command sp in order to set this directory as the one in which to save changes and/or new volumes. After that, open the desired volume using the command:

freeview -v volumename.mgz

After loading the inital volume, other volumes can either be added or loaded from the open Freeview window.

To load a new volume: Go to File>New Volume or click the new volume icon autofs/homes/011/cagnazzi/newvolumeicon.gif on the toolbar. Enter the name of the new volume in the standardized format, and make sure the selected template volume is the original volume.

To open a previously saved volume: Go to File>Load Volume, press Ctrl+O, or click the load volume icon loadvolumeicon.gif on the toolbar. The correct volume may be selected to open by navigating through the directory in the Load Volume dialogue box. Select the desired saved volume, and hit "OK."

You can explore data in a number of different viewing fields, and orientations. To see all orientations at once, including the 3D representation, choose from the toolbar on the top either 2x2 layout_2x2.gif, 1&3 layout_1n3.gif, 1&3 horizontal layout_1n3_h.gif. To have one orientation as full screen, choose the 1x1 option layout_1x1.gif. To the right of these buttons are the buttons with which you can change the orientation: saggital view_sagittal.gif, coronal view_coronal.gif, axial view_axial.gif, and 3D view_3d.gif.

You can move through the data using the mouse. Clicking on the data at a certain point will move the red crosshair to that point (as long as you are in Navigate mode, see below), the coordinates of which will be given on the bottom of the window. To scroll through slices, use Page Up and Page Down on the keyboard. To zoom in and out, use the scroll button on the mouse. To move the whole image, either click and drag using the scroll button on the mouse, or use the arrow keys on the keyboard.

In the top, left corner of the window, directly beneath the File and Edit menus you can switch between Navigate navigate.gif and Voxel Edit voxel_edit.gif modes. While in Navigate mode, you can use the mouse to move the red crosshairs and navigate through the data. Click to Voxel Edit mode, a drawing toolbox appears, and you can draw upon the volume. In the lefthand control panel, you can change Color Maps, adjust the opacity (useful when working with multiple volumes in the same window), and adjust the contrast (Window, Level, Min and Max sliding bars).

To save data and volumes, go to File>Save Volume or click the save icon savevolumeicon.gif. If it was a new volume, never before saved, it will ask you to again enter the desired volume name. Do so, and click OK. If it was a previously saved volume that you made changes to, it will continue saving under that volume name. There is a blue activity bar in the bottom right corner of Freeview. This shows the progress of loading and/or saving volumes. Be sure to wait until it is done saving before exiting Freeview. You can also check in the terminal window for a message stating that your volume has saved successfully. Note: you can continue working and making changes while it is saving, but again, be sure to save the most updated version before exiting!

Continue to FreeviewInterface for more information.

FreeviewGuide/FreeviewGeneralUsage/FreeviewQuickStart (last edited 2013-11-12 13:02:01 by MaritzaEbling)