Image Data Formats and Conversions

3dAFNItoNifTI
3dAFNItoNifTI converts AFNI .head/.brik file pairs to NifTI .nii files.

MRIConvert
MRIConvert, from the University of Oregon, is a GUI utility that converts DICOM to NifTI, Anayize, SPM99, BrainVoyager and MetaImage formats. MRIConvert includes a basic DICOM viewer. McVerter, a command line tool, is included with MRIConvert. Dcmdb uses
 * -o
 * Set output directory
 * --format=fsl
 * Output fsl formatted NifTi
 * -d
 * Save output volumes as 4D files
 * -r
 * Apply rescale slope and intercept to data
 * --nii
 * Save output files with .nii at the end.

DICOM rescale and slope are two metadata tags that describe a linear transform between how voxles are stored in memory and how they are stored on disk. The transform is
 * U is the output value
 * m rescale slope
 * SV stored value
 * b rescale intercept

The primary use of rescale and slope is with CT data. I belive modern Philips MRI scanner softare sets the slope to 1.

dcm2nii
The mricron package contains two conversion programs, dcm2nii and dcm2niigui. Dcm2nii is deprecated and should not be used for new work. If you have trouble try dcm2niix or MRIConvert.

FSLUTILS
FSL reads images in nii, nii.gz, NifTI .hdr/.imp pairs, and Analyze .hdr/.img pairs. FSLTUILS includes programs to convert, slice, merge, interleave, fix, adjust and corrupt your data. The util program fslchfiletype converts between Analyze and various types of NifTI.

DCM4CHE5
Dcm4che5 is a toolbox of command line programs to manipulate, examine and move DICOM data. Dcmdb uses findscu, movescu, and storescu to move DICOM data from PACS to /mnt/md0/dcmdb on Odin. After moving the data, dcmdb uses  to transcode from transfer syntax 1.2.840.10008.1.2.4.90 (JPEG 2000 lossless) to transfer syntax 1.2.840.10008.1.2.1 (Explicit VR little-endian uncompressed). JPEG 2000 lossless should not be confused with JPEG or .jpg files. JPEG 2000 is a compute-intensive, rarely used format. It is however how our PACSs store data internally. Transcodeing (decompressing) to transfer syntax 1.2.840.10008.1.2.1 is often a first step in processing your data with any tool set.