Instructions for installing caret (mac):
cp -r /usr/local/caret/apps/caret5.app /Applications/
Now you will have an icon that opens caret in your Applications folder.
Find the name Macaque.F99.BOTH-HEMS.STANDARD-SCENES.73730.spec
Click on the save icon to save it to disk; do not use the weird action menus. They will cause headaches. The directory (should be a directory that is downloaded, not just the spec file) can go pretty much anywhere. On the macs and linux machines in the lab, it is in /usr/local/caret/CARET_TUTORIAL_SEPT06/
(fortunately from the caret load menu /usr/local is visible).
Instructions for using caret (mac or linux):
- start up caret, either by clicking on the icon in the /Applications menu on the mac, or from the command line on both macs and linux by typing*
caret5 &
- Open up the spec file by going to the file menu > Open Spec File. On the lab machines the file that is always available is:
/usr/local/caret/CARET_TUTORIAL_SEPT06/MACAQUE/Macaque.F99.BOTH-HEMS.STANDARD-SCENES.73730.spec
On the linux machines there are also lots of other data sets available in /usr/local/caret/atlases.
The files that are spec files have the file extension: .spec. There are many more spec files and data sets that you can download from the Van Essen web site. This tutorial assumes you are using the one above, but I think they are all used in about the same way.
Once you load the spec file, a new window will open with lots of options, and you want to click “select all” towards the bottom to get all of the images, then click on “load”.
- Next, you will want to open a couple of windows so that you can have different views of the brain. To do this, go to “window” and select any number of windows. In each one, you will see something different.
- Go to one of the viewing windows, and use the menus to the right of “model” to select different things. For example, you might want 4 windows: a flatmap, an inflated map, the left hemisphere, and volume (MRI images). For all of the windows that give you the option, click YOKE. That means that when you do something to one of the images (say, rotate it), the same manipulation will be applied to all the windows, keeping them in register. If you are missing some of these maps in the “models” pulldown, it means when you loaded the spec file, you forgot to click on “select all”. Note that if you are looking at “volume” (the MRI), you can change with a pull-down menu at the top of the image whether you are looking at coronal, horizontal or sagital sections.
- Take your mouse and click somewhere. A new window will appear giving you lots of information about that spot. For example, it might say: FVE:V2 0.7. This means that according to Fellman & Van Essen, the probability that this spot is V2 is 0.7. After you do this, you will notice that a little green marker appeared on the place where you clicked (make sure you don’t double click, that erases the marker). This is really handy because you can, for example, click a place on the volume images, and then see where it is on the flat map. If you are getting too many of these and want to clear them away, look at the window where the information about areas pops up and click on: CID. This will take them all away.
- You can specify whether you want the colors on the flat map to correspond to Lewis & VanEssen coordinates or Fellman & VanEssen coordinates by clicking on the “DC” button on the main viewing window. (For some reason the main view is not listed under window, but if you go to "Bring All to Front" in the window menu, you can usually find it.) Now a new window with a whole bunch of options will come up and you may have to make the window much bigger. Click on the “Primary overlay” button adjacent to “paint”, and then scroll down the pulldown menu on the other side of "paint" to get the one you want. Then click apply. If you successfully yoked the images in step 7, the color maps will be applied to all the relevant views.
* If it is not found, you need to add /usr/local/caret/bin to your path. For instructions about paths, see HowTos.Shell
