No b0 detected, missdetection of shells

Lubomir_Vojtisek · July 1, 2020, 4:03pm

I am Trying to work on prostate data from Siemens Prisma Syngo VE11C (bvals 0, 50, 100, 200, 400, 700, 1400), but all up to b=200 are detected as one shell 105.

/Diffusion$ mrinfo -fslgrad 3211A_11d_zoomit_ep2d_diff_b50_400_800_tra.bvec 3211A_11d_zoomit_ep2d_diff_b50_400_800_tra.bval 3211A_11d_zoomit_ep2d_diff_b50_400_800_tra.nii -shell_s -shell_b
105 400 700 1400 
40 12 24 36

I have tried change parameters of .mrtrix.conf file (actually create one).

To decrease: BValueEpsilon: 10.0
It didn’t help

To simplify I have extracted just low bvals

 mrinfo  -all 3211A_dwi_den_eddy_b100.mif 
************************************************
Image:               "3211A_dwi_den_eddy_b100.mif"
************************************************
  Dimensions:        76 x 60 x 20 x 40
  Voxel size:        1.57895 x 1.57895 x 3.5 x 1
  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      -69.38
                               -0      0.9803      0.1977      -37.97
                               -0     -0.1977      0.9803      -62.86
  command_history:   dwiextract "-fslgrad" "3211A_11d_zoomit_ep2d_diff_b50_400_800_tra.bvec" "3211A_11d_zoomit_ep2d_diff_b50_400_800_tra.bval" "-shells" "100" "3211A_dwi_den_eddy.nii.gz" "3211A_dwi_den_eddy_b100.mif"  (version=3.0_RC3_latest-77-g7774aec6)
  comments:          FSL5.0
  dw_scheme:         0,0,0,0
  [40 entries]       -0.868238,0.3508306481,0.3508302119,50
                     0.862362,0.3454341057,-0.3701451199,50
                     0.868238,0.3508306481,0.3508302119,50
                     -0.862362,0.3454341057,-0.3701451199,50
                     -0.345502,0.3455022222,-0.8725004657,50
                     -0.345434,0.8623613789,-0.3701456054,50
                     -0.35083,0.8682374261,0.3508299532,50
                     -0.35083,0.3508299265,0.8682371876,50
                     0.345502,0.3455022222,-0.8725004657,50
                     0.345434,0.8623613789,-0.3701456054,50
                     0.35083,0.8682374261,0.3508299532,50
                     0.35083,0.3508299265,0.8682371876,50
                     -0.860288,0.3604882853,0.3604888628,100
                     0.860288,0.3604888628,-0.3604882853,100
                     0.860288,0.3604882853,0.3604888628,100
                     -0.860288,0.3604888628,-0.3604882853,100
                     -0.357829,0.3578289433,-0.8625057487,100
                     -0.360488,0.8602883128,-0.3604883218,100
                     -0.360488,0.8602887156,0.3604886286,100
                     -0.360489,0.3604883218,0.8602883128,100
                     0.357829,0.3578289433,-0.8625057487,100
                     0.360488,0.8602883128,-0.3604883218,100
                     0.360488,0.8602887156,0.3604886286,100
                     0.360489,0.3604883218,0.8602883128,100
                     -0.864474,0.3576054082,0.3532743508,200
                     0.861953,0.3576019992,-0.3593849071,200
                     0.864474,0.3576054082,0.3532743508,200
                     -0.861953,0.3576019992,-0.3593849071,200
                     -0.358053,0.3562832742,-0.8630530331,200
                     -0.359156,0.8614025827,-0.3591562859,200
                     -0.359169,0.8639200721,0.3530450105,200
                     -0.361831,0.3557198263,0.8617078468,200
                     0.358053,0.3562832742,-0.8630530331,200
                     0.359156,0.8614025827,-0.3591562859,200
                     0.359169,0.8639200721,0.3530450105,200
                     0.361831,0.3557198263,0.8617078468,200
                     0,0,0,0
                     0,0,0,0
                     0,0,0,0
  mrtrix_version:    3.0_RC3_latest-77-g7774aec6

Trying to debug if the config file is correct (actually I am still not sure)

mrinfo  -debug 3211A_dwi_den_eddy_b100.mif 
mrinfo: [DEBUG] No config file found at "/etc/mrtrix.conf"
mrinfo: [INFO] reading config file "/home/vojta/.mrtrix.conf"...
mrinfo: [DEBUG] reading key/value file "/home/vojta/.mrtrix.conf"...
mrinfo: [INFO] opening image "3211A_dwi_den_eddy_b100.mif"...
mrinfo: [DEBUG] reading key/value file "3211A_dwi_den_eddy_b100.mif"...
mrinfo: [DEBUG] sanitising image information...
mrinfo: [INFO] image "3211A_dwi_den_eddy_b100.mif" opened with dimensions 76x60x20x40, voxel spacing 1.5789500000000001x1.5789500000000001x3.5x1, datatype Float32LE
************************************************
Image:               "3211A_dwi_den_eddy_b100.mif"
************************************************
  Dimensions:        76 x 60 x 20 x 40
  Voxel size:        1.57895 x 1.57895 x 3.5 x 1
  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      -69.38
                               -0      0.9803      0.1977      -37.97
                               -0     -0.1977      0.9803      -62.86
  command_history:   dwiextract "-fslgrad" "3211A_11d_zoomit_ep2d_diff_b50_400_800_tra.bvec" "3211A_11d_zoomit_ep2d_diff_b50_400_800_tra.bval" "-shells" "100" "3211A_dwi_den_eddy.nii.gz" "3211A_dwi_den_eddy_b100.mif"  (version=3.0_RC3_latest-77-g7774aec6)
  comments:          FSL5.0
  dw_scheme:         0,0,0,0
  [40 entries]       -0.868238,0.3508306481,0.3508302119,50
                     ...
                     0,0,0,0

Do you please have any suggestion?
Thank you
Lubo

jdtournier · July 1, 2020, 4:21pm

Hi Lubo,

I just had a go at this, and it seems to work for me – at least using the reduced gradient table you’ve posted:

Using defaults:

$ mrinfo test.mif -shell_bvalue -shell_sizes
0 75 200 
3 24 12

Setting BValueEpsilon to 10:

$ mrinfo test.mif -shell_bvalue -shell_sizes -config BValueEpsilon 10
0 50 100 200 
3 12 12 12

Same as above without the -config BValueEpsilon 10 if I write this to my ~/.mrtrix.conf file:

BValueEpsilon: 10.0

This is using the latest release – 3.0.1, fresh from this morning
Not too sure why it’s not working on your installation…?

jdtournier · July 1, 2020, 4:31pm

Actually, I do know why this doesn’t work: the EpsilonBValue config file entry was introduced fairly recently, and only present from version 3.0.0 – you’d need to edit the code and re-build to do this in your version…