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Making a Fresh Installation of CSL ALE Software

Page history last edited by PBworks 15 years, 3 months ago

(1) Obtain Newmat11 Distribution. Obtain the beta "11" version of newmat from this page. Unpack the distribution in some new directory, e.g. a subdirectory of your home directory named "newmat", or whereever you think is good. Let's assume for the sake of illustration that this directory is named /myDir/newmat.

 

(2) Install Newmat11. Cd into /myDir/newmat. You should see a bunch of .cpp, .h, .mak, and .txt files, among a few other types. Documentation for the newmat 11 library is here. In that documentation, there's a section on how to build the library. Follow the directions for building using the gnu compiler under Unix; i.e., in that directory run the command

 

gmake -f nm_gnu.mak

 

(3) Obtain CSL ALE Distribution. Obtain the CSL ALE distribution in a gzipped tarfile here. Unpack the distribution in some new directory, e.g. a subdirectory of your home directory named "cpp", or whereever you think is good. Let's assume for the sake of illustration that this directory is named /myDir/cpp. This distribution includes not only source code for compiling binary executables but also shell scripts (*.csh and ResampleAleMapWithLinearInterpolation.tcl) as well as a stripped structural MRI to be used for overlays. Running make in this directory will create new binary executable programs.

 

(4) In the CSL ALE distribution, edit the file Makefile in a text editor. Change the 4th line so that the variable BIN_DIR points to a directory where you want the binary executables and scripts installed. Let's assume for the sake of illustration that this directory is named /myDir/bin.

 

(5) Change the 7th line in Makefile so that the variable NEWMATDIR points to whatever directory you installed newmat into, e.g. /myDir/newmat.

 

(6) Change the 11th line in Makefile so that the variable TEMPLATE_DIR points to whatever directory you want a copy of the stripped structural MRI placed, e.g. /myDir/template.

 

(7) Change the 2nd line in ResampleAleMapWithLinearInterpolation.csh so that the variable BIN_DIR points to the same directory you chose in step 4 above, e.g. /myDir/bin.

 

(8) Change the 2nd line in aleMake.csh so that the variable BIN_DIR points to the same directory you chose in step 4 above, e.g. /myDir/bin.

 

(9) Change the 2nd line in ThresholdOverlayALE.csh so that the variable TEMPLATE_DIR points to the same directory you chose in step 6 above, e.g. /myDir/template.

 

(10) Build and Install CSL ALE Software. Run the following two commands (you must have gcc installed):

 

make all

make install

 

If all goes well, the CSL ALE binary executables will be built and placed into the bin directory you indicated in step 4. Copies of the scripts will also be placed in the same directory.

 

(11) If the bin directory you indicated in step 4 is not yet in your Unix search path, run the following command:

 

set path = ( /myDir/bin $path )

 

to add the directory /myDir/bin (or whatever directory you have chosen) to your Unix search path. If you don't want to have to run this command for each new Unix session (shell) you bring up, just add the "set path" command to your .cshrc file. This file can be found in your home directory, and can be edited with a simple text editor. You can then try running the software by following the instructions found here.

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