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About

dcm_qa_ge is a simple DICOM to NIfTI validator script and dataset to test conversion of GE magnetic resonance imaging (MRI) data. Specifically, these datasets provide examples of several tags useful for research scientists.

The BIDS tag ParallelReductionFactorInPlane corresponds to the public DICOM tag Parallel Reduction Factor In-plane (0018,9069). Current GE images do not provide this tag, but the GE private tag Asset R Factors (0043,1083) does provide allow one to infer this value. Specifically, the first value of this tag corresponds to the reciprocal of this value (and the second value is the reciprocal of Parallel Reduction Factor out-of-plane (0018,9155)). Therefore, a scan with a ParallelReductionFactorInPlane of 2 will have this tag:

 (0043,1083) DS [0.5\1]

The BIDS tag MultibandAccelerationFactor is reported in the GE private tag 0043,10b6. This tag reports at multiple values, the first is the Multiband (HyperBand) Factor, the second is the Slice FOV Shift Factor, and the third refers to the Calibration Method. An example of this tag is:

(0043,10b6) LO [2\4\19\\\\]

The BIDS tag PhaseEncodingDirection combines the DICOM tags In-plane Phase Encoding Direction (0018,1312) and Rectilinear Phase Encode Reordering (0018,9034). While (0018,1312) has been provided for years, GE software Rx27 introduced reporting of (0018,9034). An example of these tags is:

(0018,1312) CS [ROW]
(0018,9034) CS [REVERSE_LINEAR]

The diffusion images were acquired on a GE 3T SIGNA Pioneer with software versions 28\LX\MR29.1_EA_2039.g by Jaemin Shin.

The fMRI images are provided to validate slice timing. The images were acquired on a GE 3T SIGNA Architect with software versions 28\LX\MR Software release:DV28.0_R02_1947.a by Brice Fernandez.

GE Slice timing

There are several possible strategies for extracting slice timing from GE DICOM images. The provided C source code slicetime.cpp demonstrates one method. Here, the DICOM header is read to determine the multi-band factor , number of slices per volume , sampling rate , sequential or interleaved order , ascending or descending order , software release (versions prior to 27.0 R3 used different mulit-band slice order) and group delay . This project can be simply compiled, e.g. c++ slicetime.cpp -o, and run by supplying the desired arguments. Note that this project is designed to determine the slice times for GE gradient-echo EPI sequences (e.g. fMRI and resting-state). The GE spin-echo sequences used for diffusion weighted images use a different pattern.

Series

  • 01_Ax_DWI_TENSOR_R2

    • Description: Axial diffusion-weighted sequence with ParallelReductionFactorInPlane of 2.

  • 02_Ax_DWI_TENSOR_R3

    • Description: Axial diffusion-weighted sequence with ParallelReductionFactorInPlane of 3.

  • 03_Ax_DWI_TENSOR_R1p5

    • Description: Axial diffusion-weighted sequence with ParallelReductionFactorInPlane of 1.5.

  • 04_Ax_DWI_TENSOR_R2MB2

    • Description: Axial diffusion-weighted sequence with ParallelReductionFactorInPlane of 2 and Multiband (HyperBand) of 2.

  • 05_3D_Ax_T1_MP_RAGE_R22

    • Description: Axial T1-weighted sequence with ParallelReductionFactorInPlane of 2 and ParallelReductionFactorOutOfPlane of 2.

  • SliceTiming\2_Ax_fMRI_HB8_72sl_int_asc

    • Description: Axial fMRI sequence, x8 Multiband, 72 slices, interleaved, ascending.

  • SliceTiming\3_Ax_fMRI_HB8_72sl_seq_asc

    • Description: Axial fMRI sequence, x8 Multiband, 72 slices, sequential, ascending.

  • SliceTiming\4_Ax_fMRI_HB8_80sl_int_asc

    • Description: Axial fMRI sequence, x8 Multiband, 80 slices, interleaved, ascending.

  • SliceTiming\5_Ax_fMRI_HB8_80sl_seq_asc

    • Description: Axial fMRI sequence, x8 Multiband, 80 slices, sequential, ascending.

  • SliceTiming\6_Ax_fMRI_HB8_77sl_int_asc

    • Description: Axial fMRI sequence, x8 Multiband, 77 slices, interleaved, ascending.

  • SliceTiming\7_Ax_fMRI_HB8_77sl_seq_asc

    • Description: Axial fMRI sequence, x8 Multiband, 77 slices, sequential, ascending.

  • SliceTiming\8_Ax_fMRI_HB8_72sl_int_des

    • Description: Axial fMRI sequence, x8 Multiband, 72 slices, interleaved, descending.

  • SliceTiming\9_Ax_fMRI_HB8_72sl_seq_des

    • Description: Axial fMRI sequence, x8 Multiband, 72 slices, sequential, descending.

  • SliceTiming\10_Ax_fMRI_HB8_80sl_int_des

    • Description: Axial fMRI sequence, x8 Multiband, 80 slices, interleaved, descending.

  • SliceTiming\11_Ax_fMRI_HB8_80sl_seq_des

    • Description: Axial fMRI sequence, x8 Multiband, 80 slices, sequential, descending.

  • SliceTiming\12_Ax_fMRI_HB8_77sl_int_des

    • Description: Axial fMRI sequence, x8 Multiband, 77 slices, interleaved, descending. Note number of slices not evenly divisible by multiband factor.

  • SliceTiming\13_Ax_fMRI_HB8_77sl_seq_des

    • Description: Axial fMRI sequence, x8 Multiband, 77 slices, sequential, descending. Note number of slices not evenly divisible by multiband factor.

  • SliceTiming\14_Ax_fMRI_HB3_48sl_int_asc

    • Description: Axial fMRI sequence, x8 Multiband, 48 slices, interleaved, ascending.

  • SliceTiming\15_Ax_fMRI_HB3_48sl_seq_asc

    • Description: Axial fMRI sequence, x8 Multiband, 48 slices, sequential, ascending.

  • SliceTimingMPh\2_fMRI_Multiphase_Des

    • Description: Axial fMRI sequence, x8 Multiband, 10 slices, sequential, descending, “Multiphase” sequence.

  • SliceTimingMPh\3_fMRI_Multiphase_Des_0.35Delay

    • Description: Axial fMRI sequence, x8 Multiband, 10 slices, sequential, descending, 350ms group delay, “Multiphase” sequence.

  • SliceTimingMPh\5_fMRI_Multiphase_Des_VariableDelays1s

    • Description: Axial fMRI sequence, x8 Multiband, 10 slices, sequential, descending, “Multiphase” sequence with variable sampling rate.

  • SliceTimingRT\2_epiRT_IntAsc_GD0

    • Description: Axial fMRI sequence, 32 slices, interleaved, ascending, no group delay, “epiRT” sequence.

  • SliceTimingRT\2_epiRT_IntAsc_GD3s

    • Description: Axial fMRI sequence, 32 slices, interleaved, ascending, 3s group delay (5s sampling rate), “epiRT” sequence.

  • SliceTimingRT\3_epiRT_IntAsc_GD33

    • Description: Axial fMRI sequence, 32 slices, interleaved, ascending, 33ms group delay, “epiRT” sequence.

  • SliceTimingRT\4_epiRT_IntAsc_GD55

    • Description: Axial fMRI sequence, 32 slices, interleaved, ascending, 55ms group delay, “epiRT” sequence.

  • SliceTimingRT\5_epiRT_IntAscHB3_GD0

    • Description: Axial fMRI sequence, x3 Multiband, 45 slices, interleaved, ascending, no group delay, “epiRT” sequence.

  • SliceTimingRT\6_epiRT_IntDesHB3_GD33

    • Description: Axial fMRI sequence, x3 Multiband, 45 slices, interleaved, descending, 33ms group delay, “epiRT” sequence.

  • SliceTimingRT\7_epiRT_IntDesHB3_GD55

    • Description: Axial fMRI sequence, x3 Multiband, 45 slices, interleaved, descending, 55ms group delay, “epiRT” sequence.