No bzero detected in HCP S1200 7T data

Hi, we encounter following problem when running dwibiascorrect on HCP S1200 7T data:

Output of failed command: dwiextract: [ERROR] No b=0 volumes present

Before running dwibiascorrect we ran mrconvert data.nii.gz -fslgrad bvecs bvals

The output of mrinfo data.mif -shell_s -shell_b prints:

60.333/15 997.11/64 1997.73/64 shells and directions.

Version: Mrtrix 3.0_RC3-96-g2c350fa9

Have you had a look at the bvecs to make sure the entries of the bzero volumes are 0,0,0?

They seem to be around -0,0,0:

mrinfo dwi.mif -all
************************************************
Image:               "dwi.mif"
************************************************
  Dimensions:        173 x 207 x 173 x 143
  Voxel size:        1.05 x 1.05 x 1.05 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       -90.6
                               -0           1           0        -126
                               -0           0           1         -72
  command_history:   mrconvert "/media/bwgig/5b18abd4-0119-4492-b321-05825dc35687/HCP1200_7T/100610/T1w/Diffusion_7T/data.nii.gz" "dwi.mif" "-fslgrad" "bvecs" "bvals"  (version=3.0_RC3-96-g2c350fa9)
  comments:          FSL5.0
  dw_scheme:         -0.028307,0.896023,-0.443105,65
  [143 entries]      -0.58252,0.068169,0.809953,980
                     -0.41278,0.840688,-0.350509,1980
                     -0.712336,-0.537862,-0.450869,990
                     -0.096517,-0.42316,-0.900899,2020
                     -0.215691,0.913182,-0.345797,1010
                     -0.90931,-0.332253,0.250526,1985
                     -0.932347,0.344028,-0.111242,1000
                     -0.216798,-0.434657,0.874112,2025
                     -0.248578,0.117181,-0.961498,975
                     -0.999498,0.010704,0.029843,60
                     -0.318398,-0.913147,-0.254529,2000
                     -0.131307,0.854283,0.502949,990
                     -0.80122,0.504602,0.321596,1990
                     -0.632602,-0.660489,0.404437,1010
                     -0.800834,0.017196,-0.59864,1980
                     -0.646936,0.415634,-0.639314,1015
                     -0.511083,0.216915,0.83171,2020
                     -0.679958,0.581063,0.447239,990
                     -0.326091,-0.86618,0.378678,2015
                     -0.05423,-0.438578,-0.897055,55
                     -0.362598,-0.929407,-0.068744,995
                     -0.798478,-0.480222,-0.363071,2005
                     -0.969117,-0.194033,0.1522,995
                     -0.323286,0.885696,0.33321,2005
                     -0.141465,-0.560866,0.815731,980
                     -0.392499,0.352243,-0.84963,1970
                     -0.223346,-0.458796,-0.860013,1015
                     -0.97463,0.206582,-0.08614,1995
                     -0.582705,0.812671,-0.004559,995
                     -0.501199,-0.284003,0.817399,65
                     -0.661619,-0.289414,0.691737,2020
                     -0.857867,-0.094613,-0.505087,990
                     -0.410265,-0.625559,-0.663595,2015
                     -0.229427,0.31424,0.921204,1015
                     -0.741797,0.569582,-0.353998,2010
                     -0.765493,-0.272701,0.582799,985
                     -0.013706,0.014315,-0.999804,1965
                     -0.194411,-0.88436,0.424397,985
                     -0.046292,0.994498,-0.093974,2005
                     -0.527373,0.819608,0.223875,60
                     -0.331067,-0.793478,-0.510674,1005
                     -0.700882,-0.706865,0.095427,1990
                     -0.304736,0.61029,-0.73122,1015
                     -0.349942,0.639566,0.684467,1980
                     -0.908718,0.225757,0.351093,990
                     -0.082805,0.723157,-0.685702,2020
                     -0.809794,-0.583097,-0.065054,995
                     -0.89369,0.08832,0.439907,2010
                     -0.558081,-0.134531,-0.818808,980
                     -0.713949,0.114961,-0.690696,55
                     -0.483853,-0.177347,-0.856992,2020
                     -0.174633,0.975928,0.130645,1000
                     -0.646571,0.761471,0.045911,2000
                     -0.228381,-0.164558,0.959564,1020
                     -0.970167,-0.190552,-0.149887,1995
                     -0.717234,0.631632,-0.294308,990
                     -0.046424,-0.826354,-0.561233,1985
                     -0.404808,0.578642,0.708028,985
                     -0.49639,-0.621993,0.605576,2015
                     -0.586765,-0.790418,-0.175917,60
                     -0.983187,-0.058447,-0.172998,995
                     -0.675635,0.350733,-0.648463,2015
                     -0.474039,-0.494817,0.728316,1015
                     -0.365483,-0.064061,0.928611,1970
                     -0.098069,-0.989349,0.107567,1005
                     -0.607977,-0.751816,-0.255217,1995
                     -0.093817,-0.170976,-0.980798,1020
                     -0.652213,0.440584,0.616849,2015
                     -0.809793,0.565885,0.154948,1000
                     -0.130403,0.42166,-0.897328,65
                     -0.02718,0.928526,-0.370272,2015
                     -0.510388,-0.449168,-0.733316,1010
                     -0.68615,-0.27872,-0.671948,2020
                     -0.61476,-0.786351,0.061017,1005
                     -0.07928,0.419377,-0.904344,2025
                     -0.498078,0.300549,-0.813381,980
                     -0.865725,0.500472,0.006948,1995
                     -0.746056,0.214863,0.630265,985
                     -0.006558,0.95583,0.293846,2000
                     -0.693459,0.296927,0.656467,65
                     -0.426626,0.818693,0.384359,1005
                     -0.754631,-0.541311,0.37083,2010
                     -0.033097,0.812786,-0.581621,985
                     -0.21036,0.347565,0.913754,1975
                     -0.855497,0.270169,-0.441739,1010
                     -0.435931,0.679479,-0.590146,1975
                     -0.000414,-0.644954,-0.764221,985
                     -0.991975,-0.010715,0.125983,1995
                     -0.865232,-0.436242,0.247119,990
                     -0.080563,-0.912756,-0.400481,60
                     -0.402133,-0.915391,0.018661,1990
                     -0.01379,0.386267,-0.922284,975
                     -0.308258,0.061404,-0.949319,1965
                     -0.892959,-0.334788,-0.3009,1005
                     -0.378278,0.925144,0.031855,1995
                     -0.139986,-0.930682,-0.337986,995
                     -0.735274,-0.011063,0.67768,2020
                     -0.456097,0.784719,-0.419752,1010
                     -0.920202,0.132886,-0.368199,1985
                     -0.731694,0.602957,-0.317911,60
                     -0.524126,-0.250669,0.813915,1015
                     -0.12331,-0.608167,-0.784173,2015
                     -0.987388,0.132732,0.086295,995
                     -0.245586,-0.733497,0.633775,1975
                     -0.562857,-0.747573,-0.3526,1000
                     -0.549193,0.700678,0.455452,2005
                     -0.402939,-0.758625,0.511985,985
                     -0.881206,-0.466558,-0.076158,2000
                     -0.500085,0.31786,0.805531,980
                     -0.760694,-0.602886,0.240569,60
                     -0.582261,0.140159,-0.80083,1975
                     -0.706714,0.110461,-0.698823,985
                     -0.467207,-0.346631,0.813366,2025
                     -0.332967,0.93981,-0.076752,1005
                     -0.417377,-0.75859,-0.500337,1985
                     -0.887767,-0.065939,0.455545,1010
                     -0.933839,0.290527,0.208662,1990
                     -0.334116,-0.188155,-0.923561,980
                     -0.606226,0.771578,-0.192763,1985
                     -0.648318,-0.342911,-0.679777,65
                     -0.392896,-0.89668,0.203954,1005
                     -0.188804,0.10947,0.975894,1970
                     -0.372163,0.716708,0.589766,1005
                     -0.867083,-0.192464,-0.459483,2005
                     -0.174233,0.015687,0.98458,1020
                     -0.570738,-0.775156,0.270908,1985
                     -0.799498,0.591975,-0.101828,1000
                     -0.209278,0.781934,0.587181,1985
                     -0.732742,-0.268182,-0.625434,1010
                     -0.219906,-0.001644,0.97552,65
                     -0.214966,0.615535,-0.758226,1970
                     -0.255168,0.478483,-0.840205,980
                     -0.857602,-0.209327,0.469789,2015
                     -0.25323,-0.660045,-0.707258,985
                     -0.37625,-0.36768,-0.850439,1975
                     -0.935288,-0.353572,-0.014942,1000
                     -0.161742,-0.972885,0.165331,2010
                     -0.627924,0.733998,0.258764,1000
                     -0.846128,0.387853,-0.365566,1985
                     -0.375979,0.904652,-0.200612,60
                     -0.68816,-0.505609,0.52038,985
                     -0.459878,0.407046,0.789193,2020
  mrtrix_version:    3.0_RC3-96-g2c350fa9

OK, I hadn’t come across these before. Their b=0 is clearly quite a bit away from zero, even though they state that they acquired b=0 images in the release notes. I’m not sure what would cause such large values here, the 3T HCP data has b=5 for their ‘b=0’ volumes. Can you double-check that the original bvals file lists the same value for the b=0 volumes…?

In any case, the simplest fix here is probably what I’d suggested in this post.

Thanks for the hint. We double-checked the bvals – they were the same.
After editing the configuration file to a b=0 threshold of 65 it worked fine.

Your link this post doesn’t work. Do you mean this one?

Thanks and best, Lucius

Thanks, good to hear. At least there’s nothing funny in our handling the bvals…

Glad to hear it. But it might be a good idea to understand why their b=0 volumes have such high b-values. Bear in mind this is a bit of a hack…

Indeed – now fixed in the original post. Thanks for pointing it out… :+1:

ok, here’s the HCP answer:

They had to increase the crusher gradient strength around the 180 degree pulses at 7T Tesla to eliminate an artifact in the b=0 images . They can’t remember now exactly what the artifact was though. But it was a serious artifact that was suppressed by the higher crusher gradients, which meant that the b=0 was b=60 in reality.

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