Processing GE MRI data with BrainVoyager 2000

This example uses  the VMR, AMR and FMR projects created from the DEPALL study scan of 20 March 2000 using the instructions in "Importing GE Data into BrainVoyager 2000".  If you are processing data for a multi-subject study you should decide at the outset whether you want to display the data in radiologic or neurologic convention.  Always verify that you have the left/right directions correct.  The AFNI program was used to verify left right in this data set.  BrainVoyager imported the GE data in neurologic convention.  The following data processing steps were done in BrainVoyager in order to get the data into corrected 3D volume time courses in Talairach space:

Apply slice time correction to FMR data.

Register FMR/AMR with VMR so that BrainVoyager knows the location and orientation of 2D slices(.fmr, .amr) with respect to the 3D anatomical image (.vmr).

Calculate AC-PC rotation and scaling to translate 3D anatomical (.vmr) into Talairach space (_tal.vmr).

Create volume time courses for 3x3x3 mm voxels in Talairach space.

Preprocess volume time courses.

We shall now cover each of these steps in detail.

Apply slice time correction to FMR data:

Open BrainVoyager and the FMR project created above(dep032000_run1.fmr).  Choose Analysis -> Data preprocessing 2D to bring up the following dialog:

Originally, only the top part of this dialog is open. Click the Advanced button to get all the options.  Make sure that only the Slice scan time correction is checked in the Preprocessing options and that Interleaved is checked in the Slice scan time correction frame.  A new FMR project file and new slice files will be created.  It's a good idea to change the Output file names to include _sc so that you now that only the slice time correction was applied. Click on the Go button.

Register FMR/AMR with VMR:

Since the later subjects in the DEPALL study were scanned from Anterior to Posterior, it is first necessary to reverse the ordering of the FMR slices in this subject which  were acquired P to A.  With the dep032000.fmr project open select the File -> Edit FMR infos menu item and click on "Reverse order" in the Edit STC file names frame:

Next click the Save to file button and the images should be reversed in the display window.

Open the dep032000_iso.vmr VMR file, choose the Spatial Transfer tab on the 3D tools dialog and use the Browse button to select the appropriate FMR project:

Next choose the Reslicing tab:

set the Tra->Cor angle to 90, the xFOV, yFOV and zFOV to 240, select Oblique 2D in the Slicing Mode frame, and set N slices to 23, Slice thickness to 7 and Gap thickness to 1 in the 2D-3D Alignment frame. The SAG view will now show the locations of the slices and the lower left image shows slice 1 from the 3D anatomical scan.  Note that it shows the nose upside down. It is necessary to set the Tra->Sag angle to 180 in the above dialog in order to orient the nose properly.

Now the 3D anatomical slice can be compared to the 2D FMR/AMR slice by clicking in the Show FMR (.AMR) box in the above dialog (or using the F11 key to toggle between the images; or F12 to overlay images).  I've found that the DEPALL orientations have all fit well with the orientations set to  Tra->Cor at 90 and Tra->Sag at 180.  Only the X, Y and Z positions have had to be adjusted slightly. This is done by selecting the 3D Coords tab in the 3D Volume tools dialog and adjusting x, y and z in the System coords frame.  The picture below shows the final values for the fit - only the z value was changed.  After obtaining a reasonably good fit click on the Spatial Transf tab and click the Save .TRF button in the Transform files frame and name the file "dep032000_2D-3D.trf"

dep032000_2D-3D.trf is a text file that looks like:

y: 128.000000
z: 148.000000
x: 128.000000
TraCor: 90.000000
TraSag: 180.000000
SagCor: 0.000000
xFoV: 240.000000
yFoV: 240.000000
zFoV: 240.000000
n_slices: 23
sl_thick: 7.000000
sl_gap: 1.000000

Talairach transformation:

Some familiarity with locating the anterior and posterior commissures is necessary to tranform the anatomical scan into Talairach space. First the 3D data (.vmr) is rotated into the acpc plane. This process is somewhat similar to the 2D-3D transformation described above.  First load the dep032000_iso.vmr anatomical scan, click on the reslicing tab on the 3D tools dialog and choose Oblique 2D in the slicing mode frame.

 This time the lower left image will show a slanted transverse view as you set the slice in the SAG view to pass through both the anterior and posterior commissures as shown below.  Notice that the Tra->Sag and Sag->Cor angles are adjusted slightly to align the brain hemispheres and that the Tra->Cor angle is set so that the white slice line passes through both the anterior and posterior commissures.  The AC and PC are both visible (as distinct U and inverted U shapes, respectively) in the reslice view in the lower left. 

Now click on the Spatial transf tab on the 3D tools dialog and the Save .TRF button in the Transform files frame to save the acpc rotation file in dep032000_acpc.trf.  In addition to saving the acpc transform it must also be applied to the image.  Click the Export .VMR button in the Apply spatial transformation frame and save the transformed data to dep032000_iso_acpc.vmr.  Next, eight reference points are chosen from this newly transformed image (dep032000_iso_acpc.vmr). The image is opened with the cross hairs marking the anterior commissure.  Click on the Talairach tab on the 3D tools dialog and choose AC from the dropdown menu in the Talairach proportional grid reference points frame then click the Set point button to record the coordinates of the AC.  Now go back to the dropdown menu and choose the PC.  Go to the 3D Coords tab and adjust y so that the cross hairs mark the posterior commissure.  Return to the Talairach tab and click Set point. Repeat this procedure to set the most anterior point AP, posterior point PP, superior point SP, inferior point IP, most left point LP, most right point RP.  Always pick the left and right points according to the L and R on the image; but note that when you use the Show point button to check your points  BrainVoyager will show the points in radiologic convention (even though the data is in neurologic convention) with RP on the left and LP on the right.  This reversal is a bit disconcerting for a neurologic example like this one but Rainer Goebel assures me that this is correct. 

Click the Save TAL button to save the talairach scaling transform file which is also a text file that looks like:

Project: D:\BVdemo\dep032000_iso_acpc.vmr
AC: 128 128 128
PC: 154 128 128
AP: 61 119 119
PP: 235 126 116
SP: 147 59 118
IP: 129 166 95
RP: 161 119 61
LP: 153 123 194

Finally click the Tal scale .VMR to save the anatomical image in Talairach space (dep032000_iso_tal.vmr).

Create volume time courses for 3x3x3 mm voxels in Talairach space:

Open dep032000_iso_tal.vmr, click on the Spatial transf tab of the 3D tools dialog, click on the Select .FMR... button in the 3D functional data frame:

Then click the Create 3D func (.VTC) in the same frame to bring up the following dialog:

Click on the Browse buttons to choose the appropriate transform and .TAL scaling files and then click the Go button.

Preprocess volume time courses:

Open the dep032000_iso_tal.vmr and choose the menu item Analysis->Use VTC file to get the following dialog:

click the browse button and choose the VTC file just created.  If you're working on a computer with lots of memory check the Load .VTC into working memory box to speed things up.  Choose Analysis->Data preprocessing 3D... from the menu bar to bring up the preprocessing choices (click Advanced to get the full range):

The default options are already checked as shown.  Click the OK button to start the processing.  Pre and post movies are made in order to visually inspect for movement and see how well it was corrected.  The log files give detailed information on the calculated motion corrections.