Hi,
my name is Marta and I am a student working on the dwi data. I am suppose to run the topup and would need help to figure out what is the phase encoding. The images were acquired on a 3 Tesla scanner Discovery MR750 (General Electric, Milwaukee, Wisconsin) using an eight-channel head coil. I have received data devided in folders based on their b- value. I have the following data set: : b0, b100, b100_AP, b500, b1000, b1500, b2000 and b2500. I opened some dicom images from b100_AP and compared them with the dicom images from folders b100 and b500. I could clearly see that images from b100_AP folder were a bit darker and more distorted which I think suggests that AP is the opposite phase encoding direction but I am not sure.
By using dcm2niix I was able to generate json file, nii.gz, bval and bvec.
According to information from json file our data have been acquired with “j” phase encoding direction; please see how my json file looks like at the the bottom of this message;I could not uploaded it here as I am a new user. Unfortunately, I cannot count on the technitian help.
It is difficult for me to understand wether our data were acquired with P=> A or A=>P phase encoding and how this can be translated into a numerical values as I need an acquisition parameters file which should look like here : https://fsl.fmrib.ox.ac.uk/fslcourse/lectures/practicals/fdt1/index.html ;see running topup.
Does the echo time stand for total readout time? So, for my data it would be 0.096?
Would my acquisition parameter file look like this:
0 -1 0 0.096
0 1 0 0.096 (opposite phase encoding)?
or rather like this:
0 1 0 0.096
0 -1 0 0.096 (opposite phase encoding)?
Is the “ImageOrientationPatientDICOM” from the json file important for the acquisition parametrs for running topup?
Please help me with this. I find interpreting the phase encoding very hard and cannot go forward without solving this matter.
JSON FILE CONTENT
{
"Modality": "MR",
"MagneticFieldStrength": 3,
"ImagingFrequency": 127.76,
"Manufacturer": "GE",
"ManufacturersModelName": "DISCOVERY_MR750w",
"PatientPosition": "HFS",
"ProcedureStepDescription": "MR_OPEN_VRAA",
"SoftwareVersions": "24_LX_MR_Software_release:DV24.0_R01_1344.a",
"MRAcquisitionType": "2D",
"SeriesDescription": "DTIs3-dir15-b1000",
"ProtocolName": "DTIs3-dir15-b1000",
"ScanningSequence": "EP_SE",
"SequenceVariant": "NONE",
"ScanOptions": "SAT_GEMS_EPI_GEMS_ART_GEMS_FILTERED_GEMS_ACC_GEMS_PFF_FS",
"ImageType": ["ORIGINAL", "PRIMARY", "OTHER"],
"SeriesNumber": 10,
"AcquisitionTime": "12:37:11.000000",
"AcquisitionNumber": 1,
"SliceThickness": 2.5,
"SpacingBetweenSlices": 2.5,
"SAR": 0.100645,
"EchoTime": 0.096,
"RepetitionTime": 9.2,
"FlipAngle": 90,
"PhaseEncodingPolarityGE": "Flipped",
"CoilString": "8HRBRAIN",
"PercentPhaseFOV": 75,
"AcquisitionMatrixPE": 100,
"ReconMatrixPE": 100,
"EffectiveEchoSpacing": 0.001036,
"TotalReadoutTime": 0.102564,
"PixelBandwidth": 5000,
"PhaseEncodingDirection": "j",
"SliceTiming": [
0,
4.784,
0.184,
4.968,
0.368,
5.152,
0.552,
5.336,
0.736,
5.52,
0.92,
5.704,
1.104,
5.888,
1.288,
6.072,
1.472,
6.256,
1.656,
6.44,
1.84,
6.624,
2.024,
6.808,
2.208,
6.992,
2.392,
7.176,
2.576,
7.36,
2.76,
7.544,
2.944,
7.728,
3.128,
7.912,
3.312,
8.096,
3.496,
8.28,
3.68,
8.464,
3.864,
8.648,
4.048,
8.832,
4.232,
9.016,
4.416,
9.2 ],
"ImageOrientationPatientDICOM": [
1,
-0,
0,
-0,
1,
0 ],
"InPlanePhaseEncodingDirectionDICOM": "COL",
"ConversionSoftware": "dcm2niix",
"ConversionSoftwareVersion": "v1.0.20190902"
}
Best regards,
Marta