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
with Caret, Surefit makes it possible to prepare and display activations
on a flattened representation of the brain. Surefit will segment
and prepare the anatomical file for Caret. Caret
will actually flatten the anatomical file, and import and overlay
the functional file. The procedures for preparing files for Surefit
and Caret can be accomplished with Afni as described here and on
the accompanying Caret page.
and Installing SUREfit
can be downloaded from the VanEssen
Labs after a simple registration process. See the Surefit
home page. Keep in mind that if you would like to display functional
activations on flat maps, you'll also want to download their program,
will install on several unix platforms (sun, sgi and linux). Identify
and download the correct set of binaries for your system. A user
manual (*.pdf) and a demo and test data set are included in the
zipped up tar file you downloaded. Select an area for the install
and untar and unzip the program. It will create a SUREfit directory
and dump everything in there. Enter the SUREfit directory and type
./INSTALL to install the program. As the program installs, it will
tell you valuable information. Especially important are the lines
to be added to your .cshrc.
that if you are also running Freesurfer from MGH, there will be
a conflict between the TCL library that SUREfit calls and the TCL
library that Freesurfer calls. On our machine, I have solved this
problem by adding two aliases to the .cshrc for each user:
surefit 'setenv TCL_LIBRARY $SFHOME/lib/tcl8.0; SureFit'
alias freesurfer 'setenv TCL_LIBRARY $FREESURFER_HOME/lib/tcl8.3;
establishing that you can start Surefit, you should go to the Caret
page on this website and setup and install Caret. The reason
for doing this now, is that the SUREfit demo and tutorial will end
by having you open and manipulate data in Caret because the programs
really work together.
out the UserManual you find in the distribution. In the data subdirectory
of your SUREfit directory, you'll find SUREFIT.DEMO and SUREFIT.TEST.
Begin with SUREFIT.DEMO and follow the instructions in the user
manual. When you are comfortable with the demo, work through the
SUREFIT.TEST data. The SUREFIT.TEST data actually has you do processing
steps that take hours, so be prepared.
your Own Data for Surefit
you import your own 3D anatomical data into Surefit, you need to
center the 3D image and align
it to the 2D anatomical (and, by extension, to the functional
image). This works for the U of A researchers because we align our
2Ds with the functionals. Other folks out there should check to
see if these techniques would be appropriate for them.
requires that the image be in MINC format, LPI orientation and have
isotropic 1x1x1 mm voxels. If you would like a copy of the centered
3dbrain, look in the Finished
Afni Tutorial Data area. Beginning with an afni *.BRIK and HEAD
file (brain3d+orig.*), run the following:
-prefix aaa brain3d+orig
afni, click "Define Datamode", select cubic resample (Anat
resam mode: Cu), select "Write Anat". Close Afni.
and the "Write Anat" command will create a resampled image
with 1x1x1 voxels.
-prefix aaa_lpi -orient LPI aaa+orig
will flip the image over into the Left-Posterior-Inferior orientation
surefit likes (Left-Posterior-Inferior refers to the corner of the
image cube that the program will use as the 0,0,0 voxel).
need to keep the resampled anatomy file in your directory when you
resample the functional image,
because afni will use the available anatomical image as a "parent"
to the functional image and give you the wrong output if it finds
the wrong anatomical parent.
will tell you the dimensions of your resampled anatomy file. For
the Study1 3D anatomical tutorial data, that should be 186x250x250.
Use the dimensions that 3dinfo reports when you run the Raw2Minc
command. Raw2Minc creates the *.mnc anatomy file for Surefit:
aaa_lpi+orig.BRIK 186 250 250
may wish to resample and flip the functional file as soon as you
are done with the anatomical file...after all, you'd be miserable
if you did all the work to segment, correct and flatten the anatomical
file and then found that there was some problem that prevented the
functional file from being resampled and flipped into the same space.
If you need an anatomical parent (with 1x1x1 voxels) for your functional
data, you should use the Afni and Raw2Minc procedures instead of
this alternative. If you only need a quick anatomical, Afni2Minc
does a nice job.
Afni2Minc command line utility will read the HEAD file and identify
the orientation and voxel size of an Afni BRIK. It will then reorient
and reslice the image, as needed to produce a *.mnc file in the
correct orientation and voxel size, e.g.,
the example, the command "Afni2Minc" is followed by the
name of a BRIK file (brain3d+orig.BRIK) to be flipped and resampled.
The command will create new files: axialized BRIK and HEAD and an
LPI *.mnc file. It will leave your original file intact. At this
point you should be able to follow the example in the DEMO and TEST
tutorials to choose a partial volume, perform segmentation, surface
render a fiducial surface prepared for flattening, and correct topological