Data Conversion
There is a plethora of spectroscopy data formats in existence. Many are vendor specific and proprietary. The fitting capabilities of FSL-MRS can be used with either NIfTI or an ASCII file format, but to access the full features of the post-processing tools data must be in the NIfTI-MRS format. To facilitate the conversion of data to this format FSL-MRS is distributed with an additional conversion tool spec2nii. Spec2nii currently converts SVS and MRSI data to NIfTI-MRS from the following formats.
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 |
Yes |
GE |
.7 (pfile) |
Yes |
No |
Yes |
UIH DICOM |
.dcm |
Yes |
Yes |
Yes |
LCModel |
.RAW |
Yes |
No |
No |
jMRUI |
.txt |
Yes |
No |
No |
jMRUI |
.mrui |
Yes |
No |
No |
ASCII |
.txt |
Yes |
No |
No |
Bruker format conversion is currently under development. The authors of the tool are happy to provide additional conversion routines if sample data and a thorough description of the format is provided. Please see the spec2nii project page on Github.
Use of spec2nii
The specific sub command (e.g. twix or dicom) must be the first argument.
To specify the creation of a JSON metadata file alongside a NIfTI file (recommended) use the -j option with any other inputs.
File names can be specified with the -f option and output directories with the -o option.
Twix
Spec2nii can be used to inspect the contents of a twix file before conversion.
spec2nii twix -v <file>
This will produce a list of the data with associated ‘evalinfo’ flags and data dimensions.
Spec2nii can then be run to convert all data from a single ‘evalinfo’ flag.
spec2nii twix -e <flag> <file>
‘Image’ is the most typically used for the main dataset. Other flags might be used for noise data, water reference data or any other use specified by the sequence programmer.
Twix format loop variables (e.g. Ave or ida) can be assigned to specific NIfTI-MRS dimensions using the -d{5,6,7} command line options. NIfTI MRS dimension tags (e.g. DIM_COIL) can be specified using the -t{5,6,7} command line options.
DICOM
Spec2nii can be passed a single file or directory of DICOM files for conversion.
spec2nii dicom <file_or_dir>
NIfTI-MRS dimension tags (e.g. DIM_COIL) can be specified using the -t command line argument.
UIH DICOM
Conversion for UIH DICOM format SVS and CSI spectroscopy.
spec2nii uih DCM_FILE_or_DIR
NIfTI MRS dimension tags (e.g. DIM_COIL) can be specified using the -t command line argument.
Philips
Conversion for Philips SDAT/SPAR files.
spec2nii philips <SDAT> <SPAR>
GE
Conversion for GE pfiles (.7).
spec2nii GE <file>
Plain text format
Conversion for text files containing one FID specified as two columns of data (real and imaginary). Required inputs are central frequency (-i, –imagingfreq; MHz), bandwidth (-b, –bandwidth; Hz). Optionally specify location with a 4x4 affine matrix passed as a plain text file (-a, –affine)
spec2nii text -i <imaging_freq> -b <bandwidth> [-a <affine>] <file>
LCModel RAW format
Conversion for .RAW text files containing one FID specified as two columns of data (real and imaginary). Optionally specify location with a 4x4 affine matrix passed as a plain text file (-a, –affine)
spec2nii raw [-a <affine>] <file>
jMRUI text format
Conversion for text files in the jMRUI format containing one FID specified as two columns of data (real and imaginary). Optionally specify location with a 4x4 affine matrix passed as a plain text file (-a, –affine)
spec2nii jmrui [-a <affine>] <file>