Thanks for that Rob. I was actually averaging the AP and PA b0’s separately and providing them to dwipreproc as -rpe_pair previously, but I’d imagine even still, you wouldn’t recommend this practice.
I tried to use the -rpe_header and -se_epi option as you suggested, but got an error saying no phase-encoding contrast present in SE-EPI images which is not what you suggested would happen.
I’m using 3.0_RC3 and python 2.7. I started with using mrconvert on the DICOMS. The acquisition is A > P. Then, because my reverse phase encoded image contains 7 b0’s and 1 b2000, I used dwiextract to keep only the b0’s in that image.I have but the details of the images below if that’s of any use.
Any ideas as to why I’m getting this error with -rpe_header? I have included the error code and headers for both the DWI and the reverse phase encoded image below if that’s of use.
Thanks so much
Paul
dwipreproc dwi_raw.mif dwi_preproc_header.mif -rpe_header -se_epi PA_b0_only.mif -eddy_options " --slm=linear " -eddy_options " --data_is_shelled "
dwipreproc:
dwipreproc: Generated temporary directory:
Command: mrconvert /home/trackhd/Desktop/TrackStorage/Paul//raw_subjects/XXX/PA_b0_only.mif /home/trackhd/Desktop/TrackStorage/Paul/yas/raw_subjects/XXX/dwipreproc-tmp-OQ8CN9/se_epi.mif
dwipreproc: Changing to temporary directory (/home/trackhd/Desktop/TrackStorage/Paul/yas/raw_subjects/XXXX/dwipreproc-tmp-OQ8CN9/)
Command: dirstat dwi.mif -output asym
dwipreproc: [WARNING] sampling of b=50 shell is strongly asymmetric; distortion correction may benefit from use of: -eddy_options " ... --slm=linear ... "
dwipreproc: [WARNING] sampling of b=299 shell is moderately asymmetric; distortion correction may benefit from use of: -eddy_options " ... --slm=linear ... "
dwipreproc: [WARNING] sampling of b=1001 shell is moderately asymmetric; distortion correction may benefit from use of: -eddy_options " ... --slm=linear ... "
dwipreproc: [ERROR] No phase-encoding contrast present in SE-EPI images; cannot perform inhomogeneity field estimation
************************************************
Image: "dwi_raw.mif"
************************************************
Dimensions: 110 x 110 x 72 x 153
Voxel size: 2 x 2 x 2 x ?
Data strides: [ -1 -2 3 4 ]
Format: MRtrix
Data type: unsigned 16 bit integer (little endian)
Intensity scaling: offset = 0, multiplier = 1
Transform: 1 0 -0 -108
0 1 -0 -93.52
-0 -0 1 -53.14
EchoTime: 0.058
FlipAngle: 88
MultibandAccelerationFactor: 2
PhaseEncodingDirection: j-
RepetitionTime: 3.26
SliceEncodingDirection: k
SliceTiming: 0,1.52750003,3.05749989,1.34749997,2.87750006,1.16750002,2.69749999,0.987500012,2.51749992,0.807500005,2.3375001,0.627499998,2.15750003,0.44749999,1.97749996,0.267500013,1.79750001,0.0874999985,1.61749995,3.14750004,1.4375,2.96749997,1.25750005,2.7874999,1.07749999,2.60750008,0.897499979,2.42750001,0.717499971,2.24749994,0.537500024,2.06750011,0.357499987,1.88750005,0.177499995,1.70749998,0,1.52750003,3.05749989,1.34749997,2.87750006,1.16750002,2.69749999,0.987500012,2.51749992,0.807500005,2.3375001,0.627499998,2.15750003,0.44749999,1.97749996,0.267500013,1.79750001,0.0874999985,1.61749995,3.14750004,1.4375,2.96749997,1.25750005,2.7874999,1.07749999,2.60750008,0.897499979,2.42750001,0.717499971,2.24749994,0.537500024,2.06750011,0.357499987,1.88750005,0.177499995,1.70749998
TotalReadoutTime: 0.0313
command_history: mrconvert "MQ04320_YAS011981469.S7/" "dwi_raw.mif" "-force" (version=3.0_RC3-51-g52a2540d)
comments: YAS011-981-469 MQ04320 (MQ04320) [MR] umnMB2p2_2mm_72sl_152+1dir_WS58-3260_4s_R016
study: [ ORIGINAL PRIMARY DIFFUSION NONE MB ND MOSAIC ]
dw_scheme: 0.57735026,-0.57735038000000005,0.57735031999999997,5
[153 entries] 0.57735026,-0.57735038000000005,0.57735031999999997,5
...
0.89165722999999997,-0.30288783000000002,-0.33646142000000001,1000
-0.02383971,-0.94302337999999997,0.33187091000000002,2005
mrtrix_version: 3.0_RC3-51-g52a2540d
And for the PA image.
************************************************
Image: "PA_b0_only.mif"
************************************************
Dimensions: 110 x 110 x 72 x 7
Voxel size: 2 x 2 x 2 x ?
Data strides: [ -1 -2 3 4 ]
Format: MRtrix
Data type: 32 bit float (little endian)
Intensity scaling: offset = 0, multiplier = 1
Transform: 1 0 -0 -108
0 1 -0 -93.52
-0 -0 1 -53.14
EchoTime: 0.058
FlipAngle: 88
MultibandAccelerationFactor: 2
PhaseEncodingDirection: j
RepetitionTime: 3.26
SliceEncodingDirection: k
SliceTiming: 0,1.52999997,3.05999994,1.35000002,2.88000011,1.16999996,2.70000005,0.99000001,2.51999998,0.810000002,2.33999991,0.629999995,2.16000009,0.449999988,1.98000002,0.270000011,1.79999995,0.0900000036,1.62,3.1500001,1.44000006,2.97000003,1.25999999,2.78999996,1.08000004,2.6099999,0.899999976,2.43000007,0.720000029,2.25,0.540000021,2.06999993,0.360000014,1.88999999,0.180000007,1.71000004,0,1.52999997,3.05999994,1.35000002,2.88000011,1.16999996,2.70000005,0.99000001,2.51999998,0.810000002,2.33999991,0.629999995,2.16000009,0.449999988,1.98000002,0.270000011,1.79999995,0.0900000036,1.62,3.1500001,1.44000006,2.97000003,1.25999999,2.78999996,1.08000004,2.6099999,0.899999976,2.43000007,0.720000029,2.25,0.540000021,2.06999993,0.360000014,1.88999999,0.180000007,1.71000004
TotalReadoutTime: 0.0313
command_history: mrconvert "MQ04320_YAS011981469.S9/" "PA_b0.mif" "-force" (version=3.0_RC3-51-g52a2540d)
dwiextract "011-981-469_PA_b0.mif" "-bzero" "011-981-469_PA_b0_only.mif" "-force" (version=3.0_RC3-51-g52a2540d)
comments: YAS011-981-469 MQ04320 (MQ04320) [MR] umnMB2p2_2mm_72sl_7+1dir_WS58-3260_b2k_BLIPREV_R016
study: [ ORIGINAL PRIMARY DIFFUSION NONE MB ND MOSAIC ]
DOS:
dw_scheme: 0.57735026,-0.57735038,0.57735032,5
[7 entries] 0.57735026,-0.57735038,0.57735032,5
...
0.57735026,-0.57735038,0.57735032,5
0.57735026,-0.57735038,0.57735032,5
mrtrix_version: 3.0_RC3-51-g52a2540d