information is very old...most machines where this stuff were
installed are gone...still, it is a lot of information, so I'd hate
to just delete it when it might be useful to someone, somewhere.
Dianne Patterson 10/25/2006
using SUREfit for segmentation and surface
rendering of the 3D anatomical file, use Caret to flatten the surface
(see the user manual) and then overlay the functional data. A series
of steps in Afni prepare fMRI BRIKs for import to Caret as Metrics
files. Finally, the Metrics files can be displayed on the different
representations of the surface in Caret.
and Installing Caret
can be downloaded from the VanEssen
Labs after a simple registration process. See the Caret
home page. Caret is available as precompiled binaries that run
on sgis, suns and linux machines. The Caret package should be dumped
into a new directory, perhaps one called "caret" and untarred
and unzipped in there (otherwise it'll spread subdirectories all
over the directory where you untar and unzip it). Enter the caret
directory and run the install program (make sure that its permissions
allow you to execute it):
the following line to the .cshrc, and source the .cshrc:
the program with the command:
tutorial datasets and the user manual are available from the caret
download site (for which you'll need a password).
Print a copy of the manual and run through the tutorials.
Your fMRI Data for Caret
will need to preprocess and analyze
your data in AFNI to the point of preparing
the clustered fico BRIK as input to Caret. The fico BRIK is a mutibucket
BRIK; that is, it stores two numerical values for each voxel. The
first value is the intensity value*. The second value is created
when you correlate the functional file to a waver
file. So each voxel of the fico BRIK contains two values: an intensity
value and a correlation value. The fico BRIK will need to be resliced,
and split into two single bucket briks (an intensity BRIK and a
correlation BRIK) in Afni. Then each bucket can be converted into
a Metrics file. Interestingly, it is the intensity BRIK that you
will likely want to overlay on the anatomical image in Caret.
the intensity information stored in the multibucket BRIK contains
intensity values only for those voxels over threshold.
the Fico BRIK
Before you run 3ddup and 3daxialize on your functional BRIKs, you
must make sure that an appropriate resliced anatomical BRIK, and
only that BRIK is available as a parent in the same directory.
-prefix study1_dup study1_block80_norm_p05_150ul+orig.
above command runs 3ddup, naming the output study1_dup. It uses
study1_block80_norm_p05_150ul+orig (from the Finished
Afni Tutorial Data area) as the input. This creates a HEAD file
only. Now start afni:
the "Define Datamode" button. Choose "Write Many"
in the lower right panel and select the file you just created with
you choose "???? resam mode: Cu", the resultant activations
will be interpolated and have their square
"Anat resam mode: NN" (Nearest neighbour) if you want
the activations to look just like the originals. This creates the
BRIK to go with the HEAD. Close and restart afni and then display
your original activations and the study1_dup file to make sure they
look the same (or at least very similar).
the Fico BRIK
-prefix study1_lpi -orient LPI study1_dup+orig
the above command we call 3daxialize with the "orient"
option (this option was added near the end of 2001, thanks to Bob
Cox, so you should have an up-to-date copy of Afni). "-prefix"
is optional, but allows you to assign a name to the output file
"-orient LPI" tells 3daxialize to flip the volume into
Caret's preferred orientation (set the origin at the Left Posterior
Inferior corner of the volume). Finally, "study1_block80_norm_p05_150ul+orig"
is the name of the file that needs to be reoriented (without specifying
"BRIK" or "HEAD").
the Multibucket Volume
-prefix study1_intensity 'study1_lpi_dup+orig'
-prefix study1_correlation 'study1_lpi_dup+orig'
two commands will create the single bucket intensity and correlation
addition to displaying your images to make sure they look right,
check them with 3dinfo. 3dinfo should reveal that each file (study1_correlation*
and study1_intensity*) has different values and one value per voxel.
However, 3dinfo will call them both Datatype fim...don't worry about
this. Check to make sure the orientation is LPI, the voxels are
1x1x1 and have the same number of voxels in each direction as in
the anatomical (186x250x250 for our study1 tutorial data). You will
probably find that it is the intensity BRIK that you will actually
want to display as an overlay in Caret.
and Displaying Metrics Files
create the metrics files, we need to feed in information about both
the fMRI file that will become the metric file AND the surface to
which it will be mapped. This means you will need to have generated
a corrected fiducial surface *.vtk file and a *.params file in surefit
before you try to run Map2Surface. Here is a hypothetical example:
the command has run, do the same for study1_correlation (if you
view the activations on a surface, open the spec file in Caret,
and make sure your new Metrics file is checked under "Metrics
"OK" and your surface should be displayed.
the Caret menu select Attributes-->Surface Coloring-->Metrics
file. You should now see your activation metrics file displayed
on the surface.