Dear Jesper,
Thanks for the answer. I changed the Total Readout Time on the acqparams.txt file and now the results of Eddy improved. For some reason the Total Readout Time that I got using MRIConvert is different from the one that I get when I use dcm2niix. Here is the information file I got from them:
MRIConvert:
Series UID: 1.3.12.2.1107.5.2.38.51004.30000017112807255160700002297
Study date: 20171128
Study time: 163414.634000
Series date: 20171128
Series time: 165641.696000
Subject: JuUl58_1
Subject birth date: 19580102
Series description: Head_ep2d_diff_p2_b800_Gdir30
Manufacturer: SIEMENS
Model name: Biograph_mMR
Software version: syngo MR E11
Study id: 0027009397
Series number: 19
Repetition time (ms): 10800
Echo time[1] (ms): 82
Flip angle: 90
Number of averages: 1
Slice thickness (mm): 2
Slice spacing (mm): 2.0000000313259
Image columns: 1040
Image rows: 1040
Phase encoding direction: COL
Voxel size x (mm): 2
Voxel size y (mm): 2
Number of volumes: 31
Number of slices: 62
Number of files: 31
Number of frames: 0
Slice duration (ms) : 173.852
Volume interval (s): 10.8
Orientation: tra
Acceleration factor: 2
Echo spacing (ms): 0.680013
Effective echo spacing (ms): 0.340007
Total readout time (FSL definition) (s): 0.0877217
Total readout time (SPM definition) (s): 0.0884017
Mosaic rows: 130
Mosaic columns: 130
Acquisition order: Other
dcm2niix:
{
"Manufacturer": "Siemens",
"ManufacturersModelName": "Biograph_mMR",
"EchoTrainLength": 53,
"AcquisitionNumber": 1,
"InstitutionName": "Klinikum_rechts_der_Isar",
"InstitutionAddress": "Ismaninger_Strasse_22_Muenchen_Muenchen_DE_81675",
"DeviceSerialNumber": "51004",
"SoftwareVersions": "syngo_MR_E11",
"ProcedureStepDescription": "PET_MR_Neurologie_(Demenz_Depression_Koma)",
"ScanningSequence": "EP",
"SequenceVariant": "SK_SP",
"SeriesDescription": "Head_ep2d_diff_p2_b800_Gdir30",
"BodyPartExamined": "HEAD",
"ProtocolName": "Head_ep2d_diff_p2_b800_Gdir30",
"SequenceName": "_ep_b0",
"ImageType": ["ORIGINAL", "PRIMARY", "DIFFUSION", "NONE", "ND", "NORM", "MOSAIC"],
"AcquisitionTime": "16:53:2.795000",
"MagneticFieldStrength": 3,
"FlipAngle": 90,
"EchoTime": 0.082,
"RepetitionTime": 10.8,
"PhaseEncodingLines": 130,
"BandwidthPerPixelPhaseEncode": 22.624,
"EffectiveEchoSpacing": 0.000340007,
"TotalReadoutTime": 0.0350207,
"AccelFactPE": 2,
"TrueEchoSpacing": 0.000680013,
"SliceTiming": [
5.39,
0,
5.565,
0.175,
5.7375,
0.3475,
5.9125,
0.5225,
6.085,
0.695,
6.26,
0.87,
6.4325,
1.0425,
6.6075,
1.2175,
6.78,
1.39,
6.955,
1.565,
7.1275,
1.74,
7.3025,
1.9125,
7.4775,
2.0875,
7.65,
2.26,
7.825,
2.435,
7.9975,
2.6075,
8.1725,
2.7825,
8.345,
2.955,
8.52,
3.13,
8.6925,
3.3025,
8.8675,
3.4775,
9.0425,
3.6525,
9.215,
3.825,
9.39,
4,
9.5625,
4.1725,
9.7375,
4.3475,
9.91,
4.52,
10.085,
4.695,
10.2575,
4.8675,
10.4325,
5.0425,
10.605,
5.215 ],
"PhaseEncodingDirection": "j-",
"ConversionSoftware": "dcm2niix",
"ConversionSoftwareVersion": "v1.0.20170724 GCC4.4.7"
}
Do you know what the reason is? I got better results with 0.0350207 s (from dcm2niix), so I guess that's right one. What do you think about it?
On the other hand, even though the corrected images look better than the original data, the voxel intensities change a lot after the eddy correction. For instance, from a range (0, 4095) to (-6984, 7225) after eddy. I suspect that something is still wrong. Have you seen something like this before?
By the way, in the question "h" of my last message I was trying to ask basically if DWI data can be corrected with either FUGUE or FEAT.
Thanks in advance for your help.
Best regards,
Aldana.
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