When mapping, make sure colname=volname, then after step 12 when you go to D/C,
then select Metric Selection from the Page Selection. Toggle among the
different colnames, and if the volumes differ, you should see different
activation patterns.
Alternatively, if you'd Replace rather than Append, you'd have only the most
recently mapped activation pattern loaded, so it would be the one you would
see,
assuming D/C overlay/underlay surface primary overlay is set to Metric.
________________________________
From: Angeline De Leon <[email protected]>
To: [email protected]
Sent: Thu, June 30, 2011 4:59:51 PM
Subject: [caret-users] Activation in metric files all look the same
Hello,
I am a new caret user and am experiencing some difficulty with properly
generating/viewing the metric file of my fMRI data. I am not sure whether I am
just not creating the metric file correctly or whether I am just not opening
the
right file. I have followed the steps in the tutorial as carefully as I could,
but am still having problems. Following is an outline of the specific steps
I've
taken:
1. Opening a spec file, Human.PALS_B12.B1-12.DEPTH_ANALYSES_LEFT.73730.spec
2. Choosing "Select All" and Loading
3. Selecting the Left Inflated view from the "Model" scroll-down bar
4. Clicking on "Attributes", "Map Volumes to Surfaces"
5. Selecting "Metric (Functional) or Surface Shape Data"
6. Checking "Enable Entry of Volume Threshold", clicking "Add Volumes from
Disk...", and entering my the values for my volume thesholding
7. In the path, selecting the thresholded volume file (file type = nii.gz) from
my data
8. Next, selecting "Map to Spec File with Atlas"
9. Opening Human.PALS_B12.B1-12.DEPTH_ANALYSES_LEFT.73730.spec as my Output
Spec File
10. In my Mapping Atlas, choosing the Space FLIRT and the Left Hemisphere as my
Atlas
11. Renaming my data_file.metric without changing any of my Data Column Names
12. Selecting Metric_Enclosing_Voxel, "Finishing", then closing
I then go to "Spec", select the "Metric" tab, and under "Metric Files" open my
data_file.metric, and select OK to "Append".
Finally, I go to "D/C", and in the "Overlay/Underlay-Surface" option in "Page
Selection", I choose "Metric" as my Data Type. In "Metric Settings", I choose
"User Scale" and specify the threshold values I used for my data.
At this point, I do see activation in the spec file uploaded into the caret
window. However, my problem is that I get this same pattern of activation for
any and every volume that I upload from my data. I don't understand why.
I am sorry for the level of detail in this email, but I am not sure which step
I
am missing or doing incorrectly. I would greatly appreciate it if someone could
please help me with this problem.
Thanks very much,
Angeline
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