[Mrtrix-discussion] FiberCup Phantom Spherical Deconvolution

[Jesse Ross-Jones]

Dear MRtrix users/Devs,

I am trying to use the spherical deconvolution method in MRtrix to
calculate the tracts in the FiberCup phantom available here:
http://www.lnao.fr/spip.php?rubrique79. I am running the commands listed
below, but am unable to successfully run *estimate_response*. Instead of
showing the progress bar to 100% I simply get: estimate_response:
estimating response function...  - ok

Do I need to modify some of the parameters or alter my approach in order to
incorporate the separate gradients?

Many thanks for the help,
Jesse

the list of commands I am running are basically the default (except for
using -grad to provide the modified gradient values):

*mrconvert *\FiberCup\6x6x6\dwi-b2650.nii dwi.mif

*average *dwi.mif -axis 3 - | threshold - - | median3D - - | median3D -
mask.mif

*dwi2tensor *dwi.mif -grad diffusion_directions_corrected_2650.txt dt.mif

*tensor2FA *dt.mif - | mrmult - mask.mif fa.mif

*tensor2vector *dt.mif - | mrmult - fa.mif ev.mif

*erode *mask.mif -npass 3 - | mrmult fa.mif - - | threshold - -abs 0.7
sf.mif

*estimate*_*response *dwi.mif sf.mif -grad
diffusion_directions_corrected_2650.txt response.txt

*csdeconv *dwi.mif response.txt -lmax 8 -mask mask.mif CSD8.mif

*streamtrack *SD_PROB CSD8.mif -seed seed.mif -mask mask.mif cst_csd.tck

A sample from diffusion_directions_corrected_2650.txt:

  0 0 0 0  1 0 0 2650  0 -0.987414 -0.158158 2650  -0.026007 -0.761231
0.64796 2650
The problem I run into is running *estimate_response *(following is the
output -debug):
*estimate_response *dwi.mif sf.mif -grad
diffusion_directions_corrected_2650.txt response.txt -debug
estimate_response [DEBUG]: reading key/value file "C:\mrtrix.conf"...
estimate_response [INFO]: opening image "dwi.mif"...
estimate_response [DEBUG]: reading key/value file ".\dwi.mif"...
estimate_response [DEBUG]: sanitising transformation matrix...
estimate_response [DEBUG]: preparing file ".\dwi.mif"
estimate_response [DEBUG]: setting up image "dwi.mif"...
estimate_response [DEBUG]: sanitising transformation matrix...
estimate_response [DEBUG]: setting up data increments for "dwi.mif"...
estimate_response [DEBUG]: data increments initialised with start = 0,
stride =
[ 1 64 -4096 4096 ]
estimate_response [INFO]: opening image "sf.mif"...
estimate_response [DEBUG]: reading key/value file ".\sf.mif"...
estimate_response [DEBUG]: sanitising transformation matrix...
estimate_response [DEBUG]: preparing file ".\sf.mif"
estimate_response [DEBUG]: setting up image "sf.mif"...
estimate_response [DEBUG]: sanitising transformation matrix...
estimate_response [DEBUG]: setting up data increments for "sf.mif"...
estimate_response [DEBUG]: data increments initialised with start = 0,
stride =
[ 1 64 -4096 ]
estimate_response [INFO]: found 65x4 diffusion-weighted encoding
estimate_response [INFO]: found b=0 images in studies [ 0 ]
estimate_response [INFO]: found 64 diffusion-weighted directions
estimate_response [INFO]: calculating even spherical harmonic components up
to o
rder 8
estimate_response [DEBUG]: mapping image "dwi.mif"...
estimate_response [DEBUG]: file ".\dwi.mif" mapped at 0x21e0000, size
532750 (re
ad-only)
estimate_response [DEBUG]: data mapper for image "dwi.mif" mapped with
segment s
ize = 266240
estimate_response [DEBUG]: mapping image "sf.mif"...
estimate_response [DEBUG]: file ".\sf.mif" mapped at 0x3d0000, size 768
(read-on
ly)
estimate_response [DEBUG]: data mapper for image "sf.mif" mapped with
segment si
ze = 4096
estimate_response [INFO]: found 0 single-fibre voxels
estimate_response: estimating response function...  - ok
estimate_response [INFO]: estimated response SH coefficients: [ nan nan nan
nan
nan ]
estimate_response [INFO]: closing image "dwi.mif"...
estimate_response [DEBUG]: unmapping file ".\dwi.mif"
estimate_response [INFO]: closing image "sf.mif"...
estimate_response [DEBUG]: unmapping file ".\sf.mif"
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