Image Data Formats and Conversions

Conversion Tools

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. Mcverter supports DICOM data from a variety of vendors including Philips, GE and Siemens. Dcmdb uses
mcverter -o --format=fsl -d -r --nii

-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 = m*SV + b

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.

dcm2niix

Dcm2niix is a rewrite and update of dcm2nii. Like dcm2nii it converts DICOM files to NIfTI. Dcm2niix can correctly convert the Philips propritary DICOM found in unusal scans that other converters struggle with. It will also handle Philips Par/Rec files. Dcm2niix is part of the MRIcroGL package and can also be downloaded from Github.

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 dcm2dcm indir outdir 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.

Image Data Formats

DICOM

DICOM is both a data format and file transfer protocols. DICOM is used for PET, MRI, CT, even dental X-Rays. Images from the scanner transfer to our PACS (Picture Image Archive Server) using DICOM. MRI data storage, search and retrival from PACS is done with DICOM. DICOM is insanly complex. DICOM meta data (information about the image) is nearly as large as the raw image data! Many meta data tags (fields) are customized by vendors. The result is a standard that is in practice a collection of private formats.