Jay,
Although I was all set to shame you into learning some scripting, John
recalled a feature that gets you around it for now. The Animate button
on the D/C: Metric: Settings menu cycles through whatever metric columns
are currently loaded. (You can load multiple volumes from disk when
mapping to the atlas; then open the resulting metric to load the
resulting columns.)
Make sure your metric scale is set to user (not auto), and press the
Animate button. You can even capture a movie of the toggling using the
File: Record main window images as movie.
Alternatively, if/when you do want individual captures, it's really not
too hard to script something like this:
----------------------------------------------------------------
#!/bin/sh
MY_VOLUMES=`ls *nii`
OUTCOMPOSITE=Composite_My_fMRI.metric
for VOLUME in `cat $MY_VOLUMES`
do
OUTROOT=`echo $VOLUME | sed 's/.nii$//g'`
caret_command -volume-map-to-surface-pals $OUTCOMPOSITE $OUTCOMPOSITE
SPM2 LEFT METRIC_INTERPOLATED_VOXEL $VOLUME -metric-afm
sed "s/COLUMN_HEAD/$COL_HEAD/g" TEMPLATE.LEFT.scene > $OUTROOT.LEFT.scene
OUTJPEG=$VOLUME.LEFT.jpg
caret_command -show-scene $SPEC $OUTROOT.LEFT.scene 1 $OUTJPEG
done
----------------------------------------------------------------
Just create a scene file that shows a single case how you like (color
scale, palette, rotation, etc.), and save it as TEMPLATE.LEFT.scene.
Then use a text editor to replace metric file in your scene with
Composite_My_fMRI.metric; also replace the column head in your sample
scene with COLUMN_HEAD. Then the above script will go through each
volume; map it; and capture that metric column in the same view as your
scene.
Donna
On 10/29/2007 09:13 AM, John Harwell wrote:
Hi Jay,
On Oct 27, 2007, at 9:06 PM, Jay Hegdé wrote:
Hi,
I have been using Caret to map functional data from SPM5 in *.nii
format onto PALS surfaces. It works without a hitch and I must say
that the results are quite spectacular! I'm sure the results would
be even better when the Caret template for SPM5 becomes available
(I'm currently using SPM2 templates).
I do have two questions, both having to do with the fact that I
need to map a relatively large number of nii files (>100) to the same
color scale. (Essentially, I need to make a time-lapse movie of the
% response change values over the course of the scan.)
(1) Is there a way I can specify the properties of color scale
(e.g., min, max, stepsize)? I need to map all my nii files using the
*same* color scale.
On the Metric:Settings page of the Display Control Dialog, is a
section titled "Color Mapping". When set to Auto Scale (the default),
the most positive metric value of the selected metric column maps to
the 1.0 value of the color palette and the most negative metric value
maps to the -1.0 value of the color palette. The problem you with
your scale is that as you change metric columns, the color shown for a
specific metric value may vary as a result of the metric columns
minimum and maximum values.
In your case, I think you want to set Color Mapping to User Scale.
With user scale, you can choose the metric values that map to 1.0 (Pos
Max) and -1.0 (Neg Max) values of the color palette. By using User
Scale, you will get a consistent mapping of metric values to the color
palette as you cycle through your 100+ metric columns.
(2) Is there a way of automating the surface mapping process
(other than using "caret_map_fmri" perhaps)? For instance, is there
a way I can record my menu selections and button presses, save it as
script, edit it as needed and run it?
Caret does not have a method of saving and replaying GUI actions as a
script. The "caret_map_fmri" program, which was intended to map
individual functional volumes to individual surfaces, will no longer
be included in future releases of Caret. However, its functionality
now part of next release of "caret_command". In addition,
caret_command is also able to map group average functional volumes to
the PALS atlas. Writing a script that maps your functional volumes is
probably the best approach. If you need the new version of
caret_command or assistance in writing a script, let us know.
Thank you very much and best regards,
Jay Hegdé
University of Minnesota
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-----------------------------------
John Harwell
[EMAIL PROTECTED]
Department of Anatomy and Neurobiology
Washington University School of Medicine
660 S. Euclid Ave Box 8108
Saint Louis, MO 63110
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