Create an MRI Project in Brain Voyager
Brain Voyager is used for imaging and statistical analysis of structural and functional MRI datasets. Here, we describe how to:
Select File|New.
The Create Project dialog box appears.
In the "Project type" panel, check the "Anatomical 3D data set (VMR)" checkbox.
If the data are in DICOM format , in the "Describe-data" panel, set the "File type" listbox to DICOM. Press the "Select first source file" button, and in the File Open dialog box, select the first source file. In the NrOfSlices text box, type in the number of .dcm files. (You can get this number in the Windows Explorer by sorting on Type, selecting all the .dcm files, and then looking in the status bar.)
If the data are in ANALYZE format , in the "Describe-data" panel, set the "File type" listbox to ANALYZE. Press the "Select first source file" button, and in the File Open dialog box, select the first source file. The NrOfSlices field gets filled in automatically.
Press the Start button.
After 5-10 seconds, the project appears as in the 3D Volume window as "untitled.vmr".
Save the VMR file, giving it an appropriate name: Select File>"Save As...", and in the File Save dialog box, give the project a name. (The initials of the subject makes a good name.)
[Possibly insert instructions about adjusting contrast and brightness here.]
Before closing the project, make 16-bit version.
NOTE: You must do this after creating the project, but before closing it. You must do this before doing the "Transform to Standard SAG" and "Isovoxel Transformation" steps.
Invoke the "16 bit 3D Data Set Tools" dialog box: Select Options>"16 bit 3D (V16) tools..." [Note: Help refers to this as Options>"Convert 16 to 8 bit intensity".]
The "16 bit 3D Data Set Tools" dialog box appears [Note: Help refers to this as the "16 Bit to 8 Bit Data Conversion" dialog box.]
The "16 bit 3D Data Set Tools" dialog box has a local File menu. Select File>"Save .v16...". , and in the File Save dialog box, give the same file name as the VMR.
Close the "16 bit 3D Data Set Tools" dialog box: Press the Quit button.
Select File|New.
The Create Project dialog box appears.
In the "Project type" panel, check the "Functional 3D data set (FMR)" checkbox.
If the data are in DICOM format , in the "Describe-data" panel, set the "File type" listbox to DICOM. Press the "Select first source file" button, and in the File Open dialog box, select the first source file. In the NrOfSlices text box, type in the number of .dcm files. (You can get this number in the Windows Explorer by sorting on Type, selecting all the .dcm files, and then looking in the status bar.)
If the data are in ANALYZE format , in the "Describe-data" panel, set the "File type" listbox to ANALYZE. Press the "Select first source file" button, and in the File Open dialog box, select the first source file. The NrOfSlices field gets filled in automatically.
Click "Select First Source File." In the appropriate driectory, select the first header (.hdr) file in the sequence.
Enter the number of Volumes (TRs). Note: you can determine this by checking the number of ".hdr" files in the folder (1 per TR).
Click on the "Advanced" button, go down to "prefix of "stc slice", and change this filed to "dir-" (i.e., the same name as the session directory).
Press the Start button.
After 5-10 seconds, the project appears as in the 2D Volume window as "untitled.fmr".
Save the FMR file, giving it an appropriate name: Select File|Save As....