Hi Dr. Schlund,
I interpret "simple overlays of functional data" as mapping functional
data onto the PALS atlas. In that case, step 1 is to take the PALS
tutorial, if you haven't already done so:
Next step is to create a SPM2-oriented visualization spec. This could
be one of the four spec files in the PALS atlas tutorial, or it could be
something more streamlined, such as the following specs:
Or it could be something in between (e.g., the streamlined + the
Next, in those starter spec files, replace the existing PALS average
fiducial coord files (711-2C atlas space) with these SPM2 versions in
your CARET_HOME/data_files/fmri_mapping_files directory/folder:
Replace them not only on the file system, but also in the spec file
(using a text editor, or by using File: Open Data File: Coord file to
open them the first time, which should add them to the spec file by
Now open that spec file and make sure the SPM2 average fiducial surface
While a MeanBuckner12 version for SPM2 does exist, you might instead
consider using the actual atlas target used (e.g., avg152T1) as the
volume anatomy file underlay for slice views. Use File: Open Data file:
Volume Anatomy file and navigate to your SPM2 templates directory to
open the appropriate volume. Make sure left appears on left.
Use File: Open Data File: Volume Functional file to open your functional
volume; select the "volume is SPM2 volume with right on left" if your
spm_defaults.m has analyze.flip=1.
Press Toolbar: D/C and select Overlay/Underlay Volume and select the
avg152T1 as underlay; your functional volume as primary overlay. They
should align well. Switch to the Settings tab and toggle on the surface
outline, if desired, to make sure the alignment between the PALS average
fiducial surface and the anatomical volume is good.
Now map the functional data onto the PALS surface:
Select Attributes: Map functional volumes to surfaces: Metric
Add loaded volumes; next
Map to spec file with atlas; select the currently loaded spec file;
Space SPM2; PALS (left or right); ok; next
Data file: change to a more meaningful output name
Mapping algorithm: Enclosing and interpolated voxel are both popular;
Toolbar: spec: metric: open the output filename you specified
D/C Overlay Underlay/Surface: primary overlay metric; select column of
Toggle between fiducial and alternative views (inflated, flat).
Over a year ago, creating space-specific visualization specs was on my
to-do list, but I'm afraid this item has been buried well below many
other priorities. If you have trouble with this step, let me know.
On 08/01/2006 08:46 AM, Michael Schlund wrote:
Caret newbie, who is very, very impressed with this software. My
is whether anyone has a SPM+caret for dummies guide available that we
might have---just a simple Word doc would be extremely helpful. We are
using SPM2 and have been having quite a bit of trouble with just the
basics of implementing caret for doing simple overlays of functional
We are using the most updated version of caret and have cruised the
website and email archives but we are still, well, floundering badly.
comments for 'how to' help would be truly spectacular.
Mike Schlund, Ph.D.
Assistant Professor, Department of Psychiatry, Johns Hopkins University
School of Medicine
Research Scientist, Department of Behavior Analysis, University of North
Faculty & Director, Neurobehavioral Imaging Laboratory, Kennedy Krieger
Adjunct Assistant Professor, Department of Psychology & Department of
Psychiatry, University of Pittsburgh
412-624-5018: [EMAIL PROTECTED], [EMAIL PROTECTED]
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