Command line tools for PET-MR (pre)-processing.
Tools for validating and extracting raw PET data, and associated files, for the purposes of image reconstruction via STIR and SIRF. Currently these tools are mainly for the Siemens mMR system and GE Signa PET/MR, although other GE PET/CT scanners should work as well.
nm_validate
The purpose of nm_validate
is to confirm if a raw data file (or file pair) contains all the expected data.
WARNING: This currently only performs additional checks on Siemens mMR data. For GE data, there are no checks on the content of the RDF.
nm_validate -i <DICOM file>
Example output for a valid list mode file:
I1205 17:15:37.418709 3333379008 NMValidate.cpp:99] Started: Tue Dec 5 17:15:37 2017
I1205 17:15:37.419257 3333379008 NMValidate.cpp:100] Running 'nm_validate' version: 0.1.0
I1205 17:15:39.136943 3333379008 Common.hpp:89] Manufacturer: SIEMENS
I1205 17:15:39.136970 3333379008 Common.hpp:97] Model name: Biograph_mMR
I1205 17:15:39.136979 3333379008 Common.hpp:105] Image type: ORIGINAL\PRIMARY\PET_LISTMODE
I1205 17:15:41.942068 3333379008 MMR.hpp:399] Expected number of LM words: 74308087
I1205 17:15:41.942098 3333379008 MMR.hpp:406] 297232348 bytes in LM field
I1205 17:15:41.942103 3333379008 MMR.hpp:410] 297232348 / 4 = 74308087 words
I1205 17:15:41.942114 3333379008 NMValidate.cpp:134] File appears to be VALID
I1205 17:15:41.942119 3333379008 NMValidate.cpp:139] Time taken: 4 seconds
I1205 17:15:41.942123 3333379008 NMValidate.cpp:140] Ended: Tue Dec 5 17:15:41 2017
nm_validate
will check list mode, sinogram and normalisation (norm) files. The size of the anticipated raw data is checked, but not the actual contents. Due to compression of the sinogram data, only the existence of files are tested.
nm_extract
Raw PET data from the mMR scanner can be in one of two forms: a single DICOM file or a pair of files (one DICOM header and a raw binary file). nm_extract
reads the DICOM data and extracts the Interfile header and the raw data for either of the two forms. Once extracted, the Interfile header can be used for image reconstruction with STIR.
GE PET scanners also store the raw data in a single DICOM file. nm_extract
reads this file and extracts the GE RDF (Raw Data Format)
file. This can then be used in STIR.
nm_extract -i <DICOM file> [-o <OUTPUTDIR> -p <PREFIX> --noupdate ]
where <DICOM file>
is the input file for extraction, <OUTPUTDIR>
is the target output directory and <PREFIX>
is the desired filename prefix for the output files. If the <OUTPUTDIR>
does not exist, nm_validate
will attempt to create it. If <OUTPUTDIR>
is not specified, the output will be written to the same directory as the input.
For Siemens data, --noupdate
will extract the raw Interfile without modification (mainly for debugging). For GE data, this option is ignored.
Siemens data:
.l
extensions for the list mode data and .l.hdr
for the associated Interfile header..s
for the sinogram data and .s.hdr
for the associated Interfile header..n
and .n.hdr
extensions.GE data:
.BLF
extension..sino.rdf
extension..norm.rdf
and .geo.rdf
extensions.nm_mrac2mu
nm_mrac2mu
extracts the patient mu-map from mMR MRAC DICOM data, scales to linear attenuation coefficients (LACs) and reslices into a full-size matrix (344 x 344 x 127) for PET reconstruction. The mu-map is oriented in LPS.
nm_mrac2mu -i <DICOMDIR> -o <OUTPUT file> [--orient <ORIENTATION> --head]
where <DICOMDIR>
is the path to the MRAC DICOM folder and <OUTPUT file>
is the destination file. <ORIENTATION>
is the desired coordinate orientation (default 'RAI'). The switch --head
will generate a mu-map in 344x344x127 matrix and is currently hard-coded for the mMR brain MRAC.
.nii.gz
e.g. myoutput.nii.gz
. .hv
is given, an Interfile header is generated in addition to the volume.nm_signa2mu
nm_signa2mu
extracts the patient mu-map from the GE Signa mMR DICOM data, scales to linear attenuation coefficients (LACs) and writes to an output file.
nm_signa2mu -i <DICOMDIR> -o <OUTPUT file> [--orient <ORIENTATION>]
where <DICOMDIR>
is the path to the MRAC DICOM folder and <OUTPUT file>
is the destination file. <ORIENTATION>
is the desired coordinate orientation (default 'RAI').
.nii.gz
e.g. myoutput.nii.gz
. .hv
is given, an Interfile header is generated in addition to the volume.