| Summary: | The Radiobiology Research Institute (RRI) package contents provide prospective gating scan modes with automated reacquisition that have been developed for efficient steady state MRI on Bruker (ParaVision 6.0.1) and Varian (VnmrJ 4.2) platforms.
The 3D methods are described in:
Kinchesh P, Gilchrist S, Beech JS, Gomes AL, Kersemans V, Newman RG, Vojnovic B, Allen PD, Brady M, Muschel RJ, Smart SC. Prospective gating control for highly efficient cardio-respiratory synchronised short and constant TR MRI in the mouse. Magn Reson Imaging 2018;53:20-27.
The SPLICER multi-slice methods are described in:
Kinchesh P, Allen PD, Gilchrist S, Kersemans V, Lanfredini S, Thapa A, O’Neill E, Smart SC. Reduced respiratory motion artefact in constant TR multi-slice MRI of the mouse. Submitted to Magn Reson Imaging.
Data showing the improved stability of the 3D methods with respect to ungated scanning can be found at http://dx.doi.org/10.5287/bodleian:a4awG5r7R.
Data showing the improved stability of a SPLICER RARE scan with respect to an ungated RARE scan are available in this repository.
RRI package scan modes include:
ge3dRRI, a 3D spoiled gradient echo scan.
bssfp3dRRI, a 3D balanced SSFP scan.
afi3dRRI, a 3D Actual Flip-angle Imaging (AFI) scan.
fseRRI/fsemsRRI, a SPLICER multi-slice fast spin echo (RARE) scan.
sgeRRI/gemsRRI, a SPLICER multi-slice spoiled gradient echo scan.
mseRRI/memsRRI, a SPLICER multi-slice multi spin echo scan.
semsRRI, a SPLICER multi-slice spin echo scan (VnmrJ 4.2 only).
The accompanying open source package software includes:
Reconstruction/conversion to NIfTI-1 format, http://nifti.nimh.nih.gov/
Generation of Flip Angle maps from AFI data.
Package Files in Repository:
PV6.0.1_RRIpkg_01.tar.gz: Package for ParaVision 6.0.1 on the Bruker AVANCE III HD console.
PV6.0.1_RRIpkg_01_INSTALL.txt: Installation instructions for PV6.0.1_RRIpkg_01.tar.gz.
VJ4.2_patches.tar.gz: Patches for VnmrJ 4.2 on the Varian VNMRS and DD2 consoles.
VJ4.2_RRIpkg_01.bsx: Self extracting package for VnmrJ 4.2 on the Varian VNMRS and DD2 consoles.
VJ4.2_RRIpkg_01_INSTALL.txt: Installation instructions for VJ4.2_RRIpkg_01.bsx.
Data Files in Repository:
SPLICER_RARE.tar.gz: SPLICER RARE vs Ungated RARE (gzipped tarfile).
SPLICER_RARE.zip: SPLICER RARE vs Ungated RARE (zipped file).
The SPLICER_RARE archives include a stability test of the SPLICER acquisition mode with 10 repeats of a 2D multi-slice RARE scan with ETL 8, effective TE 24 ms, TR 2000 ms, THK 0.5 mm, 24 contiguous slices, FOV 32 × 32 mm2 and matrix 128 × 128. For comparison, 20 repeats of an ungated scan acquired in a virtually identical scan time were acquired with otherwise identical parameters. Data were acquired on a 4.7 T 310 mm horizontal bore Biospec AVANCE III HD preclinical imaging system equipped with 114 mm bore gradient insert (Bruker BioSpin GmbH, Germany).
The files included are:
SPLICER_RARE.nii: 10 repeats of a SPLICER RARE scan.
SPLICER_RARE_mean.nii: The pixel by pixel mean of SPLICER_RARE.nii.
SPLICER_RARE_stdev.nii: The pixel by pixel standard deviation of SPLICER_RARE.nii.
SPLICER_RARE_snr.nii: The pixel by pixel SNR = SPLICER_RARE_mean.nii/SPLICER_RARE_stdev.nii.
Ungated_RARE.nii: 20 repeats of an Ungated RARE scan
Ungated_RARE_mean.nii: The pixel by pixel mean of Ungated_RARE.nii.
Ungated_RARE_stdev.nii: The pixel by pixel standard deviation of Ungated_RARE.nii.
Ungated_RARE_snr.nii: The pixel by pixel SNR = Ungated_RARE_mean.nii/Ungated_RARE_stdev.nii.
The 'nii' data are in the NIfTI-1 format, http://nifti.nimh.nih.gov/
ImageJ is a suitable viewer, http://imagej.nih.gov/ij/
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