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Subsections

A. Installing Other Software

BioImage Suite can take advantage of the presence of other software. If these are not installed some functionality will not be present (e.g. brain skull stripping which requires FSL) but the rest of BioImage Suite will function without any problems.

A.1 Installing and Configuring FSL

FSL is a software package developed at the Oxford Centre for Functional Magnetic Resonance Imaging of the Brain, It has a lot of complementary functionality to BioImage Suite and as described above BioImage Suite can invoke cleanly two modules in FSL - the Brain Extractor Tool and FAST Gray/White Segmentation tools respectively. The appropriate graphical user interfaces will only appear in the Segmentation tools is FSL is detected in your path. This involves a two step process:

Downloading and installing FSL - follow the instructions at the FSL webpage.
- Edit the configuration files fslconf.sh and fslconf.csh (located in $FSLDIR/etc/fslconf) to set the default file format to ANALYZE.
Configuring BioImage Suite to let it know where FSL is installed.
- On Linux/Mac OS X/Unix operating systems, if FSL is installed in its default location /usr/local/fsl there should be no additional configuration needed. Otherwise edit the files /usr/local/bioimagesuite/setpaths.sh and /usr/local/bioimagesuite/setpaths.csh to set FSLDIR appropriately. The relevant lines are (in setpaths.csh)
```
setenv FSLDIR /usr/local/fsl setenv FSLOUTPUTTYPE ANALYZE
```
- On Windows ...
  - FSL uses the cygwin emulation layer. You can either download this from the cygwin web page or use the version linked to from the FSL. webpage.
  - Next install FSL as usual
  - Then edit the file c: $\backslash$ yale $\backslash$ bioimagesuite $\backslash$ setpaths.bat to set both FSLDIR and CYGWINDIR. FSLDIR is the location of FSL in the unix-like path setup used by cygwin. CYGWINDIR is the location of your CYGWIN installation, typically C: $\backslash$ CYGWIN. The relevant portion of setpaths.bat is:
```
@set FSLDIR=/usr/local/fsl 
@set CYGWINDIR=c:/cygwin 
@set WFSLDIR=%CYGWINDIR%/%FSLDIR% 
@set FSLOUTPUTTYPE=ANALYZE
```

A.2 Installing the WFU Pick Atlas

The BioImage Suite uses the atlases that come with the WFU Pick Atlas Tool - this needs to be downloaded separately from www.fmri.wfumbc.edu. The easiest way to make this work with BioImage Suite is to simply uncompress the Pick Atlas software in the parent directory of BioImage Suite (e.g. c:\yale or /usr/local). Alternatively, you may set the value of the environment variable WFUATLASDIR to point to the location of this software.

Next: B. Compiling BioImage Suite Up: 9 Appendices Previous: 9 Appendices Contents