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Subsections

14. The Multi-Subject Control

14.1 Introduction

**Figure 14.1:** The BrainRegister program main menu bar.

In the BrainRegister program, the main menu (see Figure 14.1 contains options that direct the many of the software's registration, transfer, and multisubject operations. The multisubject control is a specialized tool for computing multisubject composite fMRI activation maps. It can be activate through the BrainRegister and DualMultiSubject applications - the latter has two multisubject controls to enable easy group comparisons. The multisubject control interfaces extensively with the registration tools for computing registrations and performing image comparisons etc. The BrainRegister and DualMultiSubject applications are dual-viewer applications for, among other things, computing and testing registrations. The two viewers are labeled as the Reference viewer and the Transform viewer from the role they play during registrations. The reference image is taken from the Reference viewer whereas the transform image is taken from the Transform viewer. The multisubject control leverages both these viewers and the Registration tools (accessible under the Registration menu) for its operations.

The Data Tree tool is in some respects a more generalized and updated version of this control; however for computing fMRI composite activations using the MultiSubject tool is probably more convenient.

14.2 Setup File Format

At the heart of the multisubject control is the setup file, which is stored with a ``.msb'' extension. While the setup file can be generated entirely using the graphical user interface, experienced users prefer using a text editor to edit this file directly.

A complete setup file for a group having 3 subjects and 2 tasks (or contrasts) is presented below. The text in typewriter-like font represents the setup file, whereas normal text represents comments.

Critical Note: There MUST be no spaces `` '' in any of the filenames in the setup file. This is generally a bad idea. Use underscores (``_'') instead.

1. File Header

The first line of the setup file is its header which must contain exactly the text below. Any variations to this will lead to the setup file being rejected by the application.

#Multisubject Description File v3

2. Task Definition

fMRI experiments consists of a variety of tasks/contrasts. For example, a hand motor experiment, could have tasks ``left v rest'' and ``right v rest'' respectively . The multisubject control can handle a large number of such tasks provided that they are stored in analyze-format images with filenames of the form:

Common\_PrefixTask\_SuffixCommon\_Suffix

For example for the tasks above the three tasks could be called:

/data1/study/subject22_leftvrest_tmap.hdr
/data1/study/subject22_rightvrest_tmap.hdr

where the common prefix is ``/data1/study/subject22_``, the common suffix is ``_tmap.hdr`` and the task suffices are leftvrest , and rightvrest respectively. Such a set of tasks is prescribed in the setup file as follows:

Tasks 2
- - - - - - - - - - - - - - - - - - - -
Task Name : Left vs Rest Hand Motor 
Task Suffix : leftvrest
-------------------------------------------------------
Task Name : Right vs Rest Hand Motor 
Task Suffix : rightvrest
-------------------------------------------------------

where after the word ``Tasks'' the number 2 signifies that there are two tasks, each of which is described with a descriptive ``Task Name'' and the all-important Task Suffix.

3. Individual Subject Data

Each subject is defined using upto nine pieces of information as listed below. All images must be in Analyze/NIFTI format (.hdr,.img pair or .nii.gz). The setup file stores the filenames of the images/transformations.

The Subject Id - this is the ``name'' of the subject.
The 3D Anatomical Image - the filename of a 3D image of the whole brain.
The ``2D'' Conventional (Scout) Image - a filename of the conventional anatomical image - i.e. the anatomical image acquired with the same slice-specification as the underlying fMRI study.
The Functional Image which is the filename for the first task - in this case the ``Left vs Rest Hand Motor'' task. The filename must be in the same format as that described in the Task Definition section above.
The Reference Transformation which maps the Reference/Template Brain to 3D Individual Anatomical Image . This is a non-linear registration that performs inter-brain warping.
The Internal Transformation which maps the 3D Individual Anatomical Image to the ``2D'' Conventional (Scout) Image. This is a rigid (linear) transformation which accounts for the differences in position and orientation between the two scans.
Optional: The Echoplanar Image - is either a spin echo-anatomical image which is perfectly registered with the fMRI time series, or one of the fMRI time-series images (or perhaps the mean or median T2* image).
Optional: The Distortion Transformation which maps the ``2D'' Conventional Scout Image to the Functional/Echoplanar Image . This aims to capture the distortion in the echoplanar acquisitions used for fMRI. (This is often left blank, especially if the software generating the statistical maps - the task files performs some alignment between the echoplanar and conventional images. Ideally, this should be a non-linear transformation which captures the distortion, although affine linear transformations are also often used here.
Optional: The Field Map image which is a direct measure of the distortion. This is currently not used directly, although it might be used in batch-distortion computation in the future.

Note: As shown in the example below, the appropriate line must still exist even if an optional field is blank. See for example all ``Fieldmap Image:'' lines below.

Subjects 3
- - - - - - - - - - - - - - - - - - - -
Subject Id : Subject 1
Anatomical Image : /data1/study/1256/1256.hdr 
Conventional Image : /data1/study/1256/fmri_data/conv1256_05.hdr 
Functional Image : /data1/study/1256/fmri_data/1256_leftvrest_m1.hdr 
Reference Transformation : /data1/study/registrations/template_1256_rpm.grd 
Internal Transformation : /data1/study/1256/1256_conv_1256_05.matr 
Echoplanar Image : 
Distortion Transformation : 
Fieldmap Image :
-------------------------------------------------------
Subject Id : Subject 2
Anatomical Image : /data1/study/1268/1268.hdr 
Conventional Image : /data1/study/1268/fmri_data/conv1256_05.hdr 
Functional Image : /data1/study/1268/fmri_data/1256_leftvrest_m1.hdr 
Reference Transformation : /data1/study/registrations/template_1268_rpm.grd 
Internal Transformation : /data1/study/1268/1268_conv_1256_05.matr 
Echoplanar Image : 
Distortion Transformation : 
Fieldmap Image :
-------------------------------------------------------
Subject Id : Subject 3
Anatomical Image : /data1/study/1285/1285.hdr 
Conventional Image : /data1/study/1285/fmri_data/conv1285_05.hdr 
Functional Image : /data1/study/1285/fmri_data/1285_leftvrest_m1.hdr 
Reference Transformation : /data1/study/registrations/template_1285_rpm.grd 
Internal Transformation: /data1/study/1285/1285_conv_1285_05.matr 
Echoplanar Image : 
Distortion Transformation :
Fieldmap Image :

4. Reference and Output Images

The final section in the setup file defines the Reference/Template Brain and filenames for storing the composite anatomical/functional maps.

The Reference Image (often the MNI T1 Template) defines the space for the composite maps. An additional input (VOI image) can be used to define volumes-of-interest (perhaps created using the Surface Editor application) for VOI analysis. The VOI Image has each region labeled with a unique label (e.g. 1=Left Amygdala, 2=Right Amygdala etc.)

All outputs are in the space of the reference image. The outputs are:

Average Anatomical - if desired the program can compute the average anatomical image using the transformations and the individual 3D Anatomical images.
Std Anatomical - the standard deviation of the anatomical images.
Average Functional - the average functional map image filename for the first task.
Std Functional - the standard deviation of the first task.
Tscore Functional - a t-test of the first task against zero.
Three lines marked Legacy which exist for compatibility with older versions of the multisubject control.

The filenames for the three task-dependent outputs (Average Functional, Std Functional, Tscore Functional) must be in the same format as that described in the Task Definition section above.

-------------------------------------------------------
Reference/Output Images
--------------------------------------
Reference Image : /data1/study/template/template.hdr 
VOI Image : /data1/study/template/template_vois.hdr 
Average Anatomical : /data1/study/results5/study_average_anatomical.hdr 
Std Anatomical : /data1/study/results5/study_std_anatomical.hdr 
Average Functional : /data1/study/results5/study_average_functional_leftvrest.hdr 
Std Functional: /data1/study/results5/study_std_functional_leftvrest.hdr 
Tscore Functional : /data1/study/results5/study_tmap_functional_leftvrest.hdr
Legacy : 
Legacy : 
Legacy :

14.3 The Multisubject Tool Graphical User Interface

**Figure 14.2:** The three tabs in the multisubject tool, the base (top left), the subjects (top right) and the results tab (bottom). These are described in more detail below.

This control has three tabs: ``Base'', ``Subjects'' and ``Results''. The user defines the reference brain and the tasks in the ``Base''-tab. Individual subject images/transformations can be accessed in the ``Subjects''-tab. All composite result computation/display is performed using controls in the ``Results''-tab.

The menubar contains facilities for loading/saving the setup file, loading all images, performing batch computations (best avoided, use the command line batch mode tools instead), and for interfacing to the Image Compare tool in the Registration/Overlay Control.

Important: Loading a setup file does not load the images into memory - this is to allow manipulation of the setup file without the memory/disk-access overhead involved in loading all the images for a large study. To load the images use the Load All Images menu option under the ``Images'' menu.

14.3.1 The Base Tab

This essentially consists of the Reference and VOI Image Controls and the Task definition Control, both of which are described next.

**Figure 14.3:** The Reference Image Control. A similar control (not shown) is used to manipulate the VOI Image.

The Reference Image Control

This is a common control in BioImage Suite for handling images. It consists of two textboxes, which display information about the current image and a set of buttons for manipulating the image (See Figure 14.3.)

The three textboxes display (i) the filename, (ii) the dimensions - if these are ``1 1 1'' this means that the image is not in memory, just its filename, and (iii) a detailed description of the image.

The Load button is used to load the image into memory. The Save button can be used to save the image, perhaps in a different location. The Browse button is used to define the image filename without actually loading the image. The Display Ref and Display Trn buttons display the image in the reference and transform viewers respectively. Finally the Clear button unloads and clears the image.

The setup file must be saved for changes to the image filename to be made permanent.

The VOI Image is manipulated using an identical control.

**Figure 14.4:** The Task Definition Control.

The Task Definition Control

The task definition control enables the addition/removal and editing of tasks. This relates to the Task Definition section of the setup file described earlier. As shown in Figure 14.4, this control consists of a list of tasks (left) with two associated buttons for adding a new task and removing the selected task, and a task window right for editing the task description and task suffix for the current task. Edits are acted upon when the Update button is pressed.

You may not delete the task that is currently active - this is the first task when the setup file is loaded, as this makes the setup file invalid. The current task is selected in the Results tab, described below.

14.3.2 The Subject Tab

The subjects tab, shown in the middle of Figure 14.2, is where information for each subject can be manipulated. This relates directly to the Subject Definition section of the setup file described earlier. The graphical user interface for the Subject tab is divided into a left column which contains the list of subjects and two buttons for adding a new subject and removing the currently selected subject, and the right column which displays the information for the current subject. The currently selected subject is also used by the Overlay Controls in the Results Tab (below) to determine which subject's data to overlay when the user requests ``Individual Subject'' images.

The right column of the Surface Tab contains the subject properties. The properties frame has a textbox at the top which has the name of the current subject (extracted automatically from the Anatomical Image), and then below this a nested tab control with two panes, ``Main'' and ``Distortion Correction''. Between them, these two panes contain controls for manipulating the 8 elements of the individual subject definition described above.

In the Main Tab
- Subject Id which contains the ``name'' of the Subject.
- Anatomical Image which stores the 3D Anatomical Image.
- Functional Image which stores the Functional Image for the current task.
- Transformation Anatomical - Reference which stores the Reference Transformation.
- Conventional Image which stores the ``2D'' Conventional (Scout) Image.
- Transformation Conventional - Anatomical which stores the Internal Transformation.
In the Distortion Correction Tab
- Spin-echo Echoplanar image which stores the Echoplanar image.
- Transformation Echoplanar - Conventional which stores the Distortion Transformation.
- Fieldmap Image which stores the Field Map.

Of these controls, 5 are image controls. These are similar to the reference image control shown in Figure 3. They are labeled as: The other 3 controls are transformation controls and are used to store the Reference, Internal and Distortion Transformations respectively.

**Figure 14.5:** A Transformation Control.

One of these is shown in Figure 14.5. It consists of (much like the image control shown previously) of three textboxes and a set of buttons. The three textboxes display (i) the filename, (ii) the class of the transformation (vtkTransform=linear, vtkpxComboTransform=nonlinear), and (iii) details about the transformation. If the transformation is a linear one, then the 4x4 matrix is shown in the details box. The Load button is used to load the transformation and similarly the Save button can be used to save the transformation, perhaps in a different location. The Invert button can be used to invert the transformation - use with care in the case of nonlinear transformations, and the Clear button sets the transformation to identity.

The Check button can be used to confirm the quality of the transformation. It places the original reference image (e.g. in the case of the Anatomical $\mapsto$ Reference transformation, this is the 3D Reference Image Template) in the left, or Reference Viewer, and places a resliced (warped) version of the Transform image (in this case the Anatomical image) in the Transform Viewer. The linked cursors of the two viewers can then be used to navigate to important structures and visually inspect the quality of the mapping.

The Go to Compute button sets the program for computing the transformation. It places the appropriate reference image in the Reference viewer, the appropriate Target in the Transform viewer and opens the Registration control at the appropriate tab (either linear or nonlinear). Next the user needs to click on a button in the Registration control (e.g. in the linear case either ``Rigid'' or ``Affine'', in the non-linear case ``Compute Linear + Non Linear Registration'') to start the registration. Once this is completed it can be migrated back to the multisubject tool using the Grab button. Until the Grab button is pushed the computed transformation is not stored anywhere and could be lost if the program is closed.

All modifications to the Individual subject information are saved when the Setup File is saved. Use Setup/Save Setup File button in the multisubject control to do this. It is suggested that you save the setup file periodically.

14.3.3 The Results Tab

A user, once she has finished defining the input data is defined and the registrations check, most of the time (while using the Multisubject Control!) in the Results-tab. This is divided vertically into three large units, the Compute Output frame (shown in Figure 14.6, the Output Results frame (shown in Figure 14.7) and the Output Overlay pane (see Figure 14.8). Briefly, the Compute Output frame is used to select the current task and to compute average maps. The Output Results frame can be used to directly visualize these results as well as Load/Save them to disk. The Output Overlay frame has functionality for generating anatomical/functional overlays for visualization.

**Figure 14.6:** The Compute Output Frame.

The Compute Output Frame

The Compute Output frame is shown in Figure 14.6. On the left hand side there is a frame titled ``Current Active Task'' which lets the user select the current task. The multisubject control only keeps one task in memory. To change the current task select it in the list and press the Change Current Task button. Pressing this will load the specific task files for all the subjects as well as the average, std and t-score functional maps for this task if they exist.

Composite functional maps, for the current task, are computed using the controls on the right hand side. The user may set the resolution at which these are computed (lower resolution=faster computation) as well as the interpolation mode for image reslicing. The Compute Average Functional button generates the composite maps (i.e. average functional, std functional and tscore functional). These are automatically saved if the Autosave results checkbox is enabled. Alternatively if a user desires to warp all functional data to a common frame and process them using external software, he can use the Warp Tasks to Common Space button. Both these buttons will perform their respective operations for the current task. If multiple task computations or exporting is desired, it can be accomplished using similarly named options from the Batch menu, in the multisubject control menubar. Finally, the Compute Average Image button computes the average anatomical image - this is useful as a quick visual check on the transformations.

**Figure 14.7:** The Output Results Frame.

The Output Results Frame

The Output Results frame, shown in Figure 14.7, consists of a single control, which is a multi-image control. This is a multiple image version of the standard image control used in the other tabs, e.g. see the description of the reference image control (see also shown in Figure 14.3. The only additional element is that a set of images share this control. The current image is selected from the list on the left hand side - see Figure 14.7.

**Figure 14.8:** The Overlay Controls Frame.

The Overlay Controls Frame

The overlay controls frame is a common control, also found in the Registration and DataTree tools, for creating overlays of functional data on anatomical data. The basic principle used for the overlay is that the users sets a threshold for what constitutes significant function using the Low Threshold slider and then saturates the functional data at the level set by the High Threshold slider. For more details see the description in the Registration handout.

This overlay control has three additional options over the standard overlay control.

The Output Viewer can be used to direct the overlay to either the Reference or the Transform Viewer.
The Base drop menu can be used to select which image will be used as the anatomical image on which the function is overlaid.
The Function drop menu is used to select which functional image will be used in the overlay.

If in either the Base or the Function drop menus an option marked ``Individual'' is selected, this refers to the individual anatomical/functional image from the current subject - the subject that is selected in the Subject Tab.

14.4 Examples

14.4.1 How to Overlay Activation Maps onto Anatomical Images

(a) Overlaying Common Space Tmaps onto Reference Image

**Figure 14.9:** Methods used to overlay a result map in reference space onto the reference anatomical image.
**Figure 14.10:** Methods used to overlay a result map in reference space onto the reference anatomical image - Part II.

The step-by-step instructions with reference to Figures 14.9 and 14.10 are:

Choose Brain Register from the BioImageSuite main menu. Three windows will appear: a Transform Viewer, a Reference Viewer and a BrainRegister menu bar. In the Reference Viewer choose (File | Standard Images | MNI_T1_1mm_stripped), or the filename of your chosen reference brain.
In the Transform Window choose (File | Load).
Choose the result map you wish to overlay (this map must be already saved in reference space).
On the BrainRegister menu bar choose (Help | T-distribution Table). A new window called Critical Points of the T-distribution will appear.
On the new Critical Points of the T-distribution window enter the degrees of freedom for your chosen result map. Also, enter the desired t-tailed pvalue. Use the following formulas to determine your degrees of freedom.
- Single group composite: df=#Subj-1
- Difference between two groups of subjects: df=(#SubjGrp1+#SubjGrp2)-2
On the Critical Points of the T-distribution window click the ``P(2t)-T'' button. This will calculate the T-value needed (shown in green box) for your degrees of freedom and chosen p-value.
On the BrainRegister menu bar choose (Registration | Functional Overlay). A new Registration/Overlay Tool window will appear.
On the new Registration/Overlay Tool window enter the t-value displayed on the Critical Points of the T-distribution window.
On the Registration/Overlay Tool window click ``Create Overlay''.
There are several options the user can manipulate to display different results other than the threshold. - See Figure 6a image II.
1. Overlay Type (shown in red box): Positive, Negative or Both. This toggle button changes what values of the image are displayed.
2. Colormap (shown in green box): F1, F2, F4. This toggle button changes which colormap is used to display the results. The user can change the default colormap by going back to the BioImage Suite main window and choose Preferences (as seen in Figure 1). A new BioSuite User Preference window will appear and the user can choose the desired default colormap. Then choose Save to save your default preferences.
3. Clustering (shown in purple box): This slide bar can generate a cluster size and the displayed image will contain only clusters that are greater than the chosen cluster size.

(b) Overlaying Individual Tmaps onto Individual 2D Anatomical

**Figure 14.11:** Methods used to **overlay a result map in individual space onto the individual 2D anatomical image**.

The step-by-step instructions, with reference to Figure 14.11 are:

Choose brainregister from the BioImageSuite main menu. Three windows will appear: a transform viewer, a reference window and a brainregister menu bar. In the Reference Window choose (File | Load)
Choose the filename that refers to the conventional 2D thick slice anatomical image and click Open.
In the Transform Window choose (File | Load)
Choose the task t-map or percent signal change map that is chosen to be overlaid onto the anatomical. Click Open.
On the BrainRegister menu bar Choose (Registration | Transformation). A new Registration/OverlayTool window will appear.
Under the Transformation block Click Load.
Choose the functional or echoplanar to 2D registration and Click Open. DO NOT CLICK RESLICE!
On the Registration/Overlay Tool window choose the Functional Overlay tab.
Choose your threshold
Click Create Overlay. This will reslice the functional map with the chosen registration as well as overlay the resliced image onto the anatomical and display the results in the Transform window.

14.4.2 Generating Across Subjects Composite Maps

(a) Single Group Composite Maps.

First, generate an .msb setup file as described in an earlier section of this document.

**Figure 14.12:** Methods used to generate a composite map from a single group of subjects.

The step-by-step instructions, with reference to Figure 14.12, are:

Choose brainregister or dualmultisubject from the BioImageSuite main menu. Three windows will appear: a Transform Viewer, a Reference Viewer and a BrainRegister menu bar. On the BrainRegister menu bar choose (Multisubject | Base). A new MultiSubject Tool window will appear.
On the new MultiSubject Tool window choose (Setup | Load Setup).
Choose your generated .msb file and click Open.
On the MultiSubject Tool window choose the Results Tab.
Choose your task of interest from the list of tasks then click Change Current Task. If your task of interest is the first task the program will warn you that the new task is the same as the old task. The status bar at the bottom of the window will create a blue bar increasing in length as each subject's filename is renamed to the new task. The word Done will appear next to the status bar when the renaming is complete. If you toggle back to the Subject Tab, you should see your new task in the Functional Image Filename.
On the MultiSubject Tool window click (Images | Load All Images). The status bar at the bottom of the window will create a blue bar increasing in length as the number of loaded subjects increases. The word Done will appear next to the status bar when the loading is complete.
On the MultiSubject Tool window click Compute Average Functional. The status bar at the bottom of the window will create a blue bar increasing in length as the number of subjects computed into the average increases. The word Done will appear next to the status bar when the computation is complete.
On the MultiSubject Tool window the bottom portion is labeled Output Overlay. There are several options to choose that will change the output image using three separate toggle buttons: Output Viewer, Base and Function. The Output Viewer button chooses which window (Reference or Transform) in which the output will be displayed. The Base button allows the user to choose the anatomical image on which to overlay to results. Finally, the Function button allows the user to choose between average function, t-score functional or individual functional. For purposes of this demonstration choose Output Viewer to be Transform, Base to be Reference Image and Function to be T-score of Average Functional.
Choose Threshold (See steps 4-6 on the Overlay Common Space Tmaps onto Reference Image Instructions for how to choose a threshold).
Click Create Overlay, the program will display the results in the chosen output viewer.

(b) Two Group T-test Comparisons

Generate two separate .msb files for each group as described earlier in this handout.

**Figure 14.13:** Methods used to generate a composite map from a single group of subjects - Part I.
**Figure 14.14:** Methods used to generate a composite map from a single group of subjects - Part II.

With these available, the step-by-step instructions, with reference to Figure 14.13, are:

Choose dualmultisubject from the BioImageSuite main menu. Three windows will appear: a Transform Viewer, a Reference Viewer and a BrainRegister menu bar. On the BrainRegister menu bar choose the first (Multisubject | Base). A new MultiSubject Tool window will appear.
On the new MultiSubject Tool window choose (Setup | Load Setup).
Choose your generated .msb file for your first group and click Open.
On the MultiSubject Tool window choose the Results Tab. Choose your task of interest from the list of tasks then click Change Current Task.
On the MultiSubject Tool window click (Images | Load All Images).
On the MultiSubject Tool window click Compute Average Functional.
On the BrainRegister menu bar choose the second (Multisubject2 | Base). A second MultiSubject Tool window will appear.
On the second MultiSubject Tool window choose (Setup | Load Setup).
Choose your generated .msb file for your second group and click Open.
On the MultiSubject Tool window choose the Results Tab. Choose your task of interest from the list of tasks then click Change Current Task.
On the MultiSubject Tool window click (Images | Load All Images).
On the MultiSubject Tool window click Compute Average Functional.
On either Multisubject window click the Base tab and under the Reference window click Display Reference.
On either Multisubject window under Comparisons click Show Compare Tool. A new Registration/Overlay Tool window will appear and it will be on the Compare Image tab. The filename boxes will be empty.
From the first Multisubject window (Group 1) under Comparisons click Send Mean Functional to Compare Tool as Set1. This will fill in the first filename box on the Registration/Overlay Tool window.
From the second Multisubject window (Group 2) under Comparisons click Send Mean Functional to Compare Tool as Set2. This will fill in the second filename box on the Registration/Overlay Tool window.
On the Registration/Overly Tool window click Compute Tmap. The computed functional image will be displayed in the transform window.
On the Registration/Overlay Tool window click the Functional Overlay tab.
Choose your threshold and enter it into the Low Threshold box. Refer to instructions for 5a (steps 4-8) for an explanation on how to choose a threshold.
On the Registration/Overlay Tool window click Create Overlay.

14.4.3 Creating Multi-Slice Image Displays

Once a Tmap has been overlaid onto an anatomical, it can be viewed in 3D space in the Transform window, and a separate window called the Simple Viewer can generate multi-slice images. You can accomplish this by either choosing pxitclsimpleviewer straight from the BioImageSuite menu or you can operate the same window through pxitclbrainregister or pxitcldualmultisubject.

**Figure:** Creating Multislice Displays. The snapshot shown is from an earlier version of the Simple Viewer. The newer version allows for multiple images to be displayed along different rows. See Section 14.5.

The step-by-step instructions, with reference to Figure 14.15 are:

Choose brainregister or dualmultisubject from the BioImageSuite main menu. Three windows will appear: a Transform Viewer, a Reference Viewer and a BrainRegister menu bar. Generate your image of choice with any of the above described methods. On the BrainRegister menu bar choose (Viewers | Simple Viewer). A new Simple Viewer window will appear.
On the new Simple Viewer window click ( Display | grab image from transform viewer).
Choose orientation of images by using the toggle button.
1. Axial - XY
2. Coronal - XZ
3. Sagittal - YZ
Choose how your images will be displayed.
1. Choose number of viewers or how many slices will be displayed.
2. Choose the First Slice to begin viewing your slices.
3. Choose the Increment or how many images to skip in between viewed images.
Toggle the labels On (box is red) or Off (box is the color of the background). The labels will display the slice number in image space and the orientation of the slice.
The arrows around the Zoom will allow the user to increase or decrease the image size of all slices. The user can also reshape the size of the entire window to decrease the amount of black space around each slice.
Click Save to save the image displayed on the screen. Be careful not to have the Save window over your image or you will save a figure of the Save Window instead. The file type for the image being saved can be toggled between jpeg and tiff file formats.

14.4.4 Warping single subject data to Common Space

Individual tmaps can be saved with all the transformations applied, thus being placed into the Common Reference Space.

**Figure 14.16:** Warping single subject data to common space.

The step-by-step instructions, with reference to Figure 14.16 are:

Choose brainregister or dualmultisubject from the BioImageSuite main menu. Three windows will appear: a Transform Viewer, a Reference Viewer and a BrainRegister menu bar. On the BrainRegister menu bar choose (Multisubject | Base). A new MultiSubject Tool window will appear.
On the new MultiSubject Tool window choose (Setup | Load Setup).
Choose your generated .msb file and click Open.
In the MultiSubject Tool window click (Batch | Warp to Common Space for Multiple Tasks). A new Select Tasks window will appear.
On the new Select Tasks window choose which tasks you want to warp to common space by highlighting them or just click Select All.
On the new Select Tasks window click OK. A new Select Directory window will appear.
On the new Select Directory window choose the directory for the output images. Click OK.
A new PXTkConsole will appear showing the status of the batch job. Also the Status bar at the bottom of the MultiSubject Tool window will lengthen and display what is being done. Upon completion the word Done will appear next to the Status bar.

14.5 The new SimpleViewer Tool

As of BioImage Suite 2.5, the simple viewer tool has been augmented to allow for the display of multiple images along different rows. This control ``takes'' images from the two other main viewers (Reference or Transform). The first row is always populated using the ``Grab Image from ..'' options. Additional images can be grabbed using the ``Grab Aux Image'' buttons as shown in Figure 14.17. Each auxiliary image corresponds to a row (beginning at 0 = main image) of the viewer. The ``Clear Aux Images'' option can be used to reset the viewer to single image mode. When multiple images are displayed, the number of rows is fixed to the number of images.

**Figure 14.17:** The new simple viewer tool. Two images are shown, one is the unstripped brain (top row) and the second is a stripped version (bottom row). Upto 5 different images can be displayed at once; they must have identical dimensions, e.g. everything must be in common space.

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