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Project
Neuroscience
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Main page DMN project
caret
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fsl_version_5.0.7-1~nd70+1
caret_v5.65
#
This tutorial consists of 3 parts:
I. Basic reconstruction of the brain map.
II. Changing the color of the activation.
III. Showing the insignificant activations of the other subjects from the atlas as different color.



I. To create a reconstructed brain map:


1. File/Open Spec File...
Browse the following file:
/opt/caret/data_files/standard_mesh_atlases/Human.PALS.LEFT/Human.PALS_B12.B1-12.DEPTH_ANALYSES_LEFT.73730.spec


2. Open (to choose the file from step 1.)


3. Select all


4. Load


5. Attributes/Map Volume(s) to Surface(s)


6. Metric (Functional) or Surface Shape Data


7. Next


8. Add Volumes From Disc...
Now go to directory containing the image you'd like to use in caret. For our purposes we use for example: */hla.gfeat/cope2.feat/thresh_zstat1.nii.gz
"hla" stands for "high level analysis"


9.Open (to add the file to the "Volume selection box")
It should be one entry in the "Volume selection box": "FILE - thresh_zstat1.nii.gz"


10. Map to Caret...


11. OK


12. Next


13. Next


14. Next


15. Finish


16. Close


17. D/C (button from the row below the menu bar - "Show Display Control Dialog")


18. Primary Overlay/Data Type/Metric






II. Changing the color of the activation.
NOTE: you have to have some image already loaded into caret to proceed this part.
In this part I'll explain how to change color and scale of the activation.


1. D/C (button from the row below the menu bar - "Show Display Control Dialog")


2. Page Selection/Metric Settings


3. Auto Scale - Percentage


5. Pos Min/Max 4%/96%
This setting depends on the activation. It is a metter of taste.


6. Palette/CHOOSE THE COLOR PREFFERED BY YOU




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