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Notes:
FIPS is a package for the comprehensive management of large-scale
multi-site fMRI projects, including data storage, retrieval,
calibration, analysis, multi-modal integration, and quality
control.
It provides a flexible, modular set of scripts so that the user can
set up their own standardized analysis and run it quickly on many
datasets. By default it incorporates the latest FBIRN recommended
processing stream.
FIPS is built to work with the BIRN data hierarchy, so that it can
extract data from the Human Imaging Database and the SRB. But it
can also work on your lab’s default directory structure and
database if appropriately configured. It maintains its own listing
of all the analyses it has done and all the designs it has used in
any installation, so that a single lab’s analyses can be
standardized or a multi-site effort can agree on the analysis
methods.
These analyses are also integrated with Freesurfer analyses (http://surfer.nmr.mgh.harvard.edu/fswiki) so that combined structural and functional analyses for an
individual subject can be visualized.
SYSTEM REQUIREMENTS:
•Unix (Linux or MAC OSX)
•FMRIB Software Library (FSL) 3.3.X
•FreeSurfer 4.0.X
INSTALLATION:
cd to the location where you want FIPS to be installed:
cd /place/for/software
Run:
tar xvfz fips.tar.gz
It will extract to a directory called fips.
SETTING UP THE UNIX ENVIRONMENT:
Create an enrionment variable called
setenv FIPSDIR /place/for/software/fips.
Add the path $FIPSDIR/bin to your unix path as follows:
for tcsh shell:
setenv PATH $FIPSDIR/bin:$PATH
for bash shell:
PATH="$FIPSDIR:$PATH"
Add the $FIPSDIR/fipspy to your PYTHONPATH environment variable.
Create the following environment variables:
setenv FIPS_ROOT /place/for/hierarchy/root
setenv FIPS_DB_DIR /place/for/fipsdatabase
setenv FIPS_FLAC_DIR /place/for/fipsflac
FIPS_ROOT is where the master root of the FIPS Hierarchy. All the
data that you import into the hierarchy will be located under this
directory, either directly or as symbolic links. Note that if you
use symblic links, then the amount of data storage needed directly
under this diretory (ie, on the disk hosting FIPS_ROOT) is very
small.
FIPS_DB_DIR is where the FIPS Database will reside along with a few
web pages created by FIPS and the FLAC files. The storage
requirements for this directory are small (typically less than
50MB). You may also want to place this directory in a location
where it can be shared by other users. It is strongly recommended
that this directory be backed up frequently.
FIPS_FLAC_DIR is where FIPS stores various analysis configuration
files. The storage requirements for this directory are also small
(typically less than 50MB). You may also want to place this
directory in a location where it can be shared by other users. It
is strongly recommended that this directory be backed up
frequently.
Changes:
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