OPERATING INSTRUCTIONS FOR PROTOTYPE CLINICAL AUTOALIGN PACKAGE


Introduction


This package contains the components for running basic clinical and morphometric protocols for brain imaging with automatic slice positioning. The package will install on Siemens Symphony, Quantum, Harmony or Sonata 1.5T systems with software version VA21B . A Siemens IDEA license is necessary to run the protocols.


Figure 1: Autoalign program installed in USER\CLINICAL\BRAIN\ROUTINE_auto-align



Installation


Extract the self-extracting archive Auto-Align-VA21B.exe into C:\Temp. Double-click C:\Temp\install.bat to install the autoalign package. A new program will be installed in the Exam Explorer under USER\CLINICAL\BRAIN called ROUTINE_auto-align (see Figure 1). If you experience problems during the installation, email one of the contacts listed at the end of this document.


The ROUTINE_auto-align program contains a number of standard protocols for routine brain imaging which have all been modified to work with autoalign. These protocols can be easily modified (see below).


The DIFFUSION protocol is based on an MGH modified version of the Siemens diffusion sequence, and includes a number of additional features besides autoalign. The DIFFUSION_Siemens protocol is based on the standard Siemens diffusion sequence with no modifications other than autoalign.


The MPRAGE_sag and FLASH_sag protocols are based on MGH modified versions of the Siemens tfl and gre sequences respectively. These sequences and protocols have been adapted for routine morphometry.


Operating instructions


An autoalign localizer scan is needed to calculate the position of the brain. The autoalign localizer protocol is named “auto-align_localizer” and must be collected before any of the autoaligned protocols are run. Acquisition time is 46 seconds and approximately 20 seconds are needed after collection to calculate the rigid body registration matrix that relates the position of the brain in the scanner to the autoalign atlas that is included in this package. It is essential to allow the scanner to complete the registration process before opening the next program step. The registration matrix is written to disk after the registration is complete i.e. when the “head” icon on the right of the program step queue of the acquisition window is completed. Subsequent autoaligned protocols read this registration matrix immediately when they are opened. Therefore opening an autoaligned protocol when the “head” icon is only half complete will result in incorrect positioning. Also note that the automatic positioning relates to the position of the subject’s brain when the autoalign localizer was collected. If the subject’s head moves during or after acquisition of the localizer, the automatic positioning may be invalid. The autoalign localizer may be reacquired at any time during the protocol.


Subsequent scans will read the registration matrix from the disk, and positioning will be done automatically as soon as the protocol is opened. Automatic positioning can be switched on and off on the special card of the user interface. An additional offset relative to the atlas may be selected and saved with the protocol. The clinical protocol is set up with a fixed offset of 15 degrees clockwise around the right-left axis relative to the atlas. Positioning will be parallel or perpendicular to the midline, and approximately parallel or perpendicular to AC-PC. However, AC-PC is not a consistent landmark between subjects. The registration algorithm aligns the brain globally to the atlas. Therefore positioning relative to AC-PC may vary between subjects. This reflects true anatomical variation between subjects and is not an artifact of the registration algorithm.


Special card of the autoalign localizer


Shown in Figure 2 is the special card of the autoalign localizer.



Figure 2: Special card of autoalign localizer



The first and second flip angles of the autoalign localizer should always be set to 2 deg. and 6 deg. respectively. For routine use, the “Generate matrix” option should be set to “Yes”. The localizer will always create two series of images, one for each flip angle, but if “Generate matrix” is set to “No”, it will not create a registration matrix. If autoaligned protocols are executed in this case, whatever registration matrix happens to be saved on disk from a previous subject will be used. The “Raw save” option should always be set to “Off”. The reconstruction code that saves raw data is not included in this package, and acquisition will fail if the “Raw save” option is enabled.


Special card of autoaligned protocols



Figure 3: Special card of autoaligned protocol



Figure 3 shows the part of the special card of an autoaligned sequence that is relevant to automatic positioning. The “Auto-set prescription” selection box can be set to “Inactive”, “Autoalign” or “Autocorrect”. “Autocorrect” functionality is not included in this package and should not be selected. Selecting “Inactive” will disable automatic alignment, and allow the user to adjust the slice positioning with the user interface as usual without automatic positioning. If “Autoalign” is selected, positioning will be done automatically, and repositioning on the UI will not be possible. If the operator wishes to change the positioning that autoalign selects, autoalign should be disabled here before the operator manually changes the slice prescription.


The “Load/save pat. prot.” option is not implemented in this distribution.


“In-plane rotation” refers to the ability to rotate the prescription within the plane of its main orientation. This is not possible by default from the UI with double-oblique slice positioning. “In-plane rotation” should normally be set to “Disable”. Automatic position will still rotate the prescription in-plane even when the option is set to “Disable”. Setting “In-plane rotation” to “Enable” will enable the operator to alter the in-plane rotation i.e. if the operator changes the number of degrees set in the second “In-plane rotation” box, this will be reflected in the slice prescription. In order to change the in-plane rotation manually, “Auto-set prescription” should be set to “Inactive”.


Setting the positioning relative to the atlas


The autoalign atlas is arranged so that the default automatic orientation with no relative offset is perpendicular or parallel to the midline, but the rotation in the sagittal plane (or tilt between coronal and transverse planes) is arbitrary (but fixed). The default positioning is approximately 15 deg. counter-clockwise of AC-PC along the right-left axis, but AC-PC is itself somewhat variable relative to the brain as a whole and is therefore not a reliable reference. The clinical protocols in this distribution are set up with the 15 deg. offset included.


The offset relative to the atlas is described by a rigid body transformation matrix. The value of this matrix is encapsulated in the “Rel. position/orientation” array. This array contains the three translations, relative to the sagittal, coronal and transverse planes (“Rel. position S”, “Rel. position C” and “Rel. position T” respectively). It also contains the orientation in the form of the first two vectors of a 3x3 rigid body rotation matrix (expressed in “Rel. orientation 00” through “Rel. orientation 02”, and “Rel. orientation 10” through “Rel. orientation 12”). Since the matrix is orthonormal, the third vector is the cross product of the first two vectors and need not be specified explicitly. The rotation matrix is expressed in the RAS coordinate system.


Rather than calculating the translations and rotation matrix explicitly, an easier method to set the offsets is via the user interface. One way is the following using the graphical slice positioning tool (not the exam explorer):

  1. Disable autoalign by setting “Auto-set prescription” to “Inactive”.

  2. Adjust the prescription on the UI by dragging the positioning box(es) to the desired orientation.

  3. Save the prescription to the protocol by setting “Copy prescr. to prot.” to “Copy” and then immediately back to “Preserve” (this simulates the action of a push-button, which is not available on the special card). Note that the relative position and orientation values in the array are updated.

  4. Reenable autoalign by setting “Auto-set prescription” to “Autoalign”. The positioning should not change from the desired setting.

  5. To save the new protocol, drag it back from the the queued scans to the Exam Explorer (this can only be done once an acquisition with the scan has been started).


Alternatively, step 2 can be replaced by explicitly setting the prescription numerically on the “Routine” card under “Position” and “Orientation”. By writing the identity matrix to the text file “RegMatrixFile.txt” in “Q:\TempAutoslice”, positioning relative to the atlas can be simulated. This is the manner in which the clinical protocols were set up. An identity matrix is provided in the file “IdentityRegMatrixFile.txt”. To copy the identity matrix before modifying protocols, open a command prompt window and type “copy Q:\TempAutoslice\IdentityRegMatrixFile.txt Q:\TempAutoslice\RegMatrixFile.txt”, or open the Windows NT Explorer and perform the same task.


References


[1] Van der Kouwe, A., et al., Proc ISMRM (11), 797, 2003.

[2] Itti, L., Chang, L., Ernst, T., Magn Reson Med 45:486-494, 2001.

[3] Welch, E.B., et al., Proc ISMRM 1:377, 2002.

[4] Fischl, B., et al., Neuron 33:341-355, 2002.


Contacts


André van der Kouwe (<andre@nmr.mgh.harvard.edu>)

Thomas Benner (<thomas.benner@nmr.mgh.harvard.edu>)


Athinoula A. Martinos Center for Biomedical Imaging

Room 2301

Building 149, 13th Street

Charlestown

MA 02129, U.S.A.