Importing GE MRI data into BrainVoyager 2000
This example uses the DEPALL study scan of 20 March 2000 to first create a BrainVoyager 3D anatomical image (.vmr), next to create a set of 2D anatomical images coincident with the EPI slice images (.amr), and finally to import the muiltislice EPI images into a functional MRI data set (.fmr). You will need the Excel spreadsheet form that lists all the scanning parameters in order to give BrainVoyager the necessary image parameters.
Creating a BrainVoyager 3D anatomical image (.vmr) data set:
Scan 2, the 3D whole brain T1 anatomical scan, consists of 124 slices contained in GE formatted files I.001 to I.124. After opening BV use File->New to open the Create Project dialog:
choose GE_I for data file type, check 3D data set (.vmr) in Project type, make sure the target directory is set and click on select first file. This will automatically fill in some of the boxes (Delimiter, X resolution, Y resolution, and Extension). Type 124 for NrOfSlices and click the start button. After reading data from all 124 files the following image is shown:
We can see from the above image that the slices aren't arranged properly in
the display boxes. Open the 3D Volume Tools by clicking on the box icon 
,
choose the Spatial transf. tab and click on To SAG button.
The Transform to Standard SAG dialog will open. Choose the sketch that represents the view currently in the sagittal view box and hit the Rearrange button. The slices will be moved to the proper views except that the sagittal view will be inverted. Choose To SAG again, check the proper sketch and hit Rearrange. The Transform to Standard SAG dialog is also used to set whether the image data is in Radiologic or Neurologic convention. A comparison of the transverse slice to the same slice displayed in AFNI (this data has already been analyzed in AFNI) revealed that the Neurologic convention properly labeled Left/Right.
Referring to the scan sheet we can see that in the x and y directions, 24 cm corresponds to 256 voxels = 0.94 millimeter and in the z direction the thickness is 1.1 mm. Choose Iso-voxel from 3D tools (just below the To SAG button and set the X,Y,Z dimensions to 0.94, 0.94 and 1.1 mm respectively:
The final image should look like:
and can now be saved. Notice that the left/right labels are in the neurologic convention.
Creating a BrainVoyager 2D anatomical (.amr) data set:
Scan 4, the 2D whole brain T1 anatomical scan, consists of 23 slices contained in GE formatted files I.001 to I.023. These high resolution images are coincident with the EPI functional slices and are used by BrainVoyager to overlay the low resolution functional slices. Since BrainVoyager can't read GE's parameters describing the positioning of the EPI slices relative to the 3D anatomical image coordinates, the AMR is useful for manually fitting the 2D slices to the 3D anatomical and determining these values. Creating the BrainVoyager 2D anatomical (.amr) is similar to the description above for the 3D anatomical. Start with the Create Project with project set to Anatomical MRI volume (.amr):
Make sure the Data file type is set to GE_I; select the first file I.001 from
the S4 folder; set the number of slices to 23 and the target directory to where
you are saving the BV data, then click on Start. The AMR window initially
shows only the first slice. More slices can be viewed by using the add
column 
and add row 
buttons.
Note that these are coronal slices scanned from posterior to anterior.
Creating a BrainVoyager FMRI (.fmr) data set:
Scan 6 is a multislice EPI functional scan consisting of 23 coronal slices, 7 mm thick with 1 mm spacing and 64 x 64 samples in the XY directions. The TR is 3 seconds and 414 scans were completed in 1242 seconds (20:42) with the data saved in a binary P file. Frequency space data in the P files is converted to images by the program erfmri_recon which saves the 23 images per volume by 409 volumes (the first 5 T1 saturated volumes are dropped) into a single (.sdt) file. BrainVoyager has been set up to accept .sdt files as a user defined data type.
As with the anatomical scan use File->New to open the create project dialog and check Project type Functional MRI data set (.fmr):
Click the Select first source file.. button and choose the proper .sdt file. Make sure the Data file type has been set to sdt, NrOfSlices to 23, NrOfVolumes to 409, target directory is set properly, and Prefix of .stc files to run1_slice-. Then click the Start button. The 409 binary volume images are read in by BrainVoyager and stored as 23 slice files each containing the 409 images of that slice. A .fmr file which references the slice (.stc) files is also saved. BrainVoyager displays an fmr project as:
Clicking on any of the slice voxels brings up a plot of the time course for that voxel:
A region of voxels can also be selected to bring up a plot of the average time course for the selected voxels. These data are now ready
for further processing and analysis by BrainVoyager.
With the FMR project open choose the File->Edit FMR Infos menu to open the following dialog:
Click the browse button and choose dep032000.amr as the AMR reference file. These high resolution slice images are overlaid on the FMR with the following result:
January, 2001: A Perl script has been written to automatically create VMR and AMR projects. It can be obtained from Larry and needs to be put in your PC's C:\WINDOWS directory (or somewhere in $PATH). In order to run it, open a DOS command window and change to the directory containing the image files (S2 for VMR, S4 for AMR) and type bv-load -vmr or bv-load -amr and the script will automatically start BrainVoyager and load in the appropriate image files. For the VMR project BrainVoyager will be open at the stage of the second figure above showing the sagittal, coronal and transverse images, so that the steps to get the image into the correct orientation with isovoxels must still be done. The AMR project can be saved into an appropriately named file without any further processing.