No bzero detected in HCP S1200 7T data

preprocessing

#1

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


#2

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


#3

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

#4

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.


#5

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


#6

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:


#7

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.