spec2nii 0.2.9

Multi-format in vivo MR spectroscopy conversion to NIFTI

spec2nii

A program for multi-format in vivo MR spectroscopy conversion to NIFTI.

Installation

pip install spec2nii

Currently supported formats

This table lists the currently supported formats. I have very limited experience with Philips and GE formats. Please get in touch if you are willing to help add to this list and/or supply validation data.

Format	File extension	SVS	CSI	Automatic orientation
Siemens Twix	.dat	Yes	No	Yes
Siemens DICOM	.ima / .dcm	Yes	Yes	Yes
Philips	.SPAR/.SDAT	Yes	No	No
GE	.7 (pfile)	Yes	No	No
LCModel	.RAW	Yes	No	No
jMRUI	.txt	Yes	No	No
ASCII	.txt	Yes	No	No

Instructions

spec2nii is called on the comandline, and the conversion file type is specified with a subcommand.

The -f and -o options specify output file name and directory respectively for all formats.

If -j is specified a sidecar JSON file containing usefull meta data will be generated from the file headers. This is similar to the BIDs format.

Twix

spec2nii twix Call spec2nii twix -v FILE to view a list of contained MDH flags. -m can be used to specify which multi-raid file to convert if used on VE data.

Call with the -e flag to specify which MDH flag to convert. e.g.
spec2nii twix -e image FILE

DICOM

spec2nii dicom DCM_FILE_or_DIR

GE (limited support)

spec2nii GE FILE

Philips (limited support)

spec2nii GE SDAT_FILE SPAR_FILE

Text/LCModel/jMRUI

Conversion from processed formats. All take an optional -a argument to specify a text file containing a 4x4 affine matrix specifying orientation information.

The text format requires additional information, namely imaging frequency in MHz and bandwidth in hertz.

spec2nii raw -a AFFINE_FILE FILE
spec2nii jmrui -a AFFINE_FILE FILE
spec2nii text -a AFFINE_FILE -i imaging_freq -b bandwidth FILE