Hi,
I’ll check the best way to send you the images, and I let you know.
Can you confirm both images have the same dimensions too…?
I was checking this and I found something that maybe could be related with this:
when I run mrinfo in the raw image, converted to dicom using dcm2niix:
************************************************
Image: "8018-750.nii.gz"
************************************************
Dimensions: 128 x 128 x 56 x 72
Voxel size: 2 x 2 x 2 x 3.4
Data strides: [ -1 2 3 4 ]
Format: NIfTI-1.1 (GZip compressed)
Data type: signed 16 bit integer (little endian)
Intensity scaling: offset = 0, multiplier = 1
Transform: 1 0 -3.16e-13 -121.1
0 1 -2.924e-11 -165.1
3.16e-13 2.924e-11 1 -65.28
comments: TE=78;Time=135201.870;phase=0;mb=2
Now mrinfo in the same image, in the dicom file:
mrinfo: [done] scanning DICOM folder "../Dicom/7_DTI_Neonate_v6_pt1/"
mrinfo: [100%] reading DICOM series "DTI_Neonate_v6_pt1"
mrinfo: [WARNING] Number of entries in mosaic slice timing (101) does not match number of images in mosaic (56); omitting
************************************************
Image: "ANONYMISED (8018) [MR] DTI_Neonate_v6_pt1"
************************************************
Dimensions: 128 x 128 x 56 x 72
Voxel size: 2 x 2 x 2 x ?
Data strides: [ -1 -2 3 4 ]
Format: DICOM
Data type: unsigned 16 bit integer (little endian)
Intensity scaling: offset = 0, multiplier = 1
Transform: 1 0 -3.16e-13 -121.1
0 1 -2.924e-11 -165.1
3.16e-13 2.924e-11 1 -65.28
EchoTime: 0.078
FlipAngle: 90
PhaseEncodingDirection: i
RepetitionTime: 3.4
TotalReadoutTime: 0.0499
dw_scheme: 0,0,0,0
[72 entries] 0,0,0,0
...
0.50580150000000001,-0.34587522999999998,0.79027528000000002,750
-0.27290904999999999,0.17999113999999999,0.94505238999999996,750
Now for the phase encode reversed:
Nifti:
************************************************
Image: "8018-REV.nii.gz"
************************************************
Dimensions: 128 x 128 x 56 x 3
Voxel size: 2 x 2 x 2 x 3.4
Data strides: [ -1 2 3 4 ]
Format: NIfTI-1.1 (GZip compressed)
Data type: signed 16 bit integer (little endian)
Intensity scaling: offset = 0, multiplier = 1
Transform: 1 -4.897e-12 -3.16e-13 -121.1
4.897e-12 1 -2.924e-11 -165.1
3.16e-13 2.924e-11 1 -65.28
comments: TE=78;Time=135132.263;phase=1;mb=2
Dicom:
mrinfo: [done] scanning DICOM folder "../Dicom/6_DTI_Neonate_v6_rev/"
mrinfo: [100%] reading DICOM series "DTI_Neonate_v6_rev"
************************************************
Image: "ANONYMISED (8018) [MR] DTI_Neonate_v6_rev"
************************************************
Dimensions: 128 x 128 x 56 x 3
Voxel size: 2 x 2 x 2 x ?
Data strides: [ -1 -2 3 4 ]
Format: DICOM
Data type: unsigned 16 bit integer (little endian)
Intensity scaling: offset = 0, multiplier = 1
Transform: 1 -4.897e-12 -3.16e-13 -121.1
4.897e-12 1 -2.924e-11 -165.1
3.16e-13 2.924e-11 1 -65.28
EchoTime: 0.078
FlipAngle: 90
MultibandAccelerationFactor: 1
PhaseEncodingDirection: i-
RepetitionTime: 3.4
SliceEncodingDirection: k
SliceTiming: 3.33249998,0,3.4525001,0.1175,3.56999993,0.237499997,3.69000006,0.357499987,3.80999994,0.474999994,3.92750001,0.595000029,4.04750013,0.712499976,4.16499996,0.832499981,4.28499985,0.952499986,4.40500021,1.07000005,4.52250004,1.19000006,4.64249992,1.3075,4.76000023,1.42750001,4.88000011,1.54750001,5,1.66499996,5.11749983,1.78499997,5.23750019,1.90499997,5.35750008,2.02250004,5.4749999,2.14249992,5.59499979,2.25999999,5.7125001,2.38000011,5.83249998,2.5,5.95249987,2.61750007,6.07000017,2.73749995,6.19000006,2.85750008,6.30999994,2.9749999,6.42749977,3.09500003,6.54750013,3.2125001
TotalReadoutTime: 0.0495
dw_scheme: 0,0,0,0
0,0,0,0
0,0,0,0
It looks like the MultibandAccelerationFactor
is 1 in the reversed image (obtained from the dicom) and 2 from the nifti. Could be this the reason?
Best regards,
Manuel