Downloading
To download the NPAIRS software along with some sample data, click here. The downloaded file is a 19 megabyte compressed tar file.
Installing
The filename of the downloaded file is NPAIRS-xxxx.tgz, where xxxx is a random 4 digit number. Move this file to where you want to install the NPAIRS package (~19 MB). To extract the contents of the file issue the following command:
tar -vzxf NPAIRS-xxxx.tgz
This will create a directory called NPAIRS-i.j, where i,j are that major and minor revision numbers, respectively. All the files in the tar file will be dumped to this directory.
To run the NPAIRS software, IDL must know where to find the programs (.pro files). This is done by setting the system variable IDL_PATH to include the directory where the NPAIRS programs exist:
unix> setenv IDL_PATH "/..../NPAIRS-1.0/pro:$IDL_PATH"
This will add the NPAIRS directory to the already existing set of IDL directories to be searched. Note, you can move the NPAIRS pro directory anywhere on your file system, you just have to make sure the IDL search path has been modified to reflect the new location.
Sample Data
The NPAIRS distribution comes with a sample data set. This is an O-15 PET data set consisting of 8 subjects. Each subject was scanned 8 times while performing a left handed finger opposition task. Scans 1, 3, 5, 7 are baselines, and scans 2, 4, 6, 8 are activations. The scans for each subject were motion corrected, aligned to a Talairach template volume, and smoothed with a 3x3x3 boxcar filter. The data is saved in the data/vols directory as one file per volume (total of 64) in VAPET format. One mask volume exists for each of the 8 subjects and are saved in the data/msks directory. A reference MRI template volume (in VAPET format) is saved in data/refVol with filename ref_vol_T1_128x128x48.mri. This volume is the same size (dimension 128 x 128 x 48, voxel size 0.31293 x 0.31293 x 0.3375 cm's) as the data volumes and is spatially aligned to them. Finally, there is a volume list file for the data set in the directory data/lists.
A CVA NPAIRS and GLM NPAIRS analyses were run on this sample data and the results saved in example/cva and example/glm, respectively. The NPAIRS ID is ex1_8FO_cva_DEMO for the CVA analysis, and ex1_8FO_glm_DEMO for the GLM analysis. In the instructions on how to run NPAIRS, an example will be given for each step. Following this example through to the end will result in the running of two NPAIRS anlyses, one for a CVA and one for a GLM, with ID's ex1_8FO_cva and ex1_8FO_glm, respectively. These two analyses should give the same results as the DEMO analyses.