[Mrtrix-discussion] dwi2response failed to find SH peak

[Robert Smith]

Hi,

The "failed to find SH peak!" error is not entirely uncommon, especially if
the input mask contains some non-brain voxels.

It's a little hidden, but the problem lies here:
dwi2response [INFO]: Initial response function is [331.3299255 -81.32884216]
This indicates that the algorithm is using lmax = 2: this makes it
impossible to identify voxels with crossing fibres and remove them from the
single-fibre mask, so the algorithm will take much longer (normally
dwi2response runs CSD only on the single-fibre voxels from the previous
iteration, so each subsequent iteration takes less time).

I would take a close look at your gradient table (presumably already stored
as a bvecs/bvals pair or external MRtrix format text file, given you are
using compressed niftis). It's possible that the table is either corrupt,
or is being erroneously split into two b-value shells when in reality only
one is present:
dwi2response [INFO]: Diffusion gradient encoding data clustered into 2
shells
It also appears to not include any b=0 volumes (not that that should
matter, the command won't use the b=0's, it's just slightly unusual to not
have any).

If the problem's not immediately obvious, feel free to copy & paste the
file contents here. I'll also add some extra debugging outputs / sanity
checks to the code to hopefully give more interpretable feedback in such
circumstances.

Cheers
Rob


--

*Robert Smith, Ph.D*
Research Officer, Imaging Division

The Florey Institute of Neuroscience and Mental Health
Melbourne Brain Centre - Austin Campus
245 Burgundy Street
Heidelberg Vic 3084
Ph: +61 3 9035 7128
Fax: +61 3 9035 7301
www.florey.edu.au

On Tue, Nov 25, 2014 at 2:11 AM, Rafa X <rromero3000 at gmail.com> wrote:

>  Hi Mrtrix expert,
> I'm new on mrtrix and I'm trying to run dwi2response (using -grad) but it
> has been days in a loop that said "failed to find SH peak!". Below you can
> see the output provided by "-info -debug".
>
>
>  dwi2response [INFO]: opening image
> "/home/rr480/Code/KirstieDTI/SUB_DATA/22566/DTI/MRI0/dti_ec.nii.gz"...
> dwi2response [DEBUG]: sanitising image information...
> dwi2response [DEBUG]: voxel accessor for image
> "/home/rr480/Code/KirstieDTI/SUB_DATA/22566/DTI/MRI0/dti_ec.nii.gz"
> initialised with start = 95, strides = [ -1 96 9216 ]
> dwi2response [INFO]: opening image
> "/home/rr480/Code/KirstieDTI/SUB_DATA/22566/DTI/MRI0/dti_ec_brain_mask.nii.gz"...
> dwi2response [DEBUG]: sanitising image information...
> dwi2response [DEBUG]: loading image
> "/home/rr480/Code/KirstieDTI/SUB_DATA/22566/DTI/MRI0/dti_ec_brain_mask.nii.gz"...
> dwi2response: uncompressing image
> "/home/rr480/Code/KirstieDTI/SUB_DATA/22566/DTI/MRI0/dti_ec_brain_mask.nii.gz"...
> 100%
> dwi2response [DEBUG]: image
> "/home/rr480/Code/KirstieDTI/SUB_DATA/22566/DTI/MRI0/dti_ec_brain_mask.nii.gz"
> loaded
> dwi2response [DEBUG]: voxel accessor for image
> "/home/rr480/Code/KirstieDTI/SUB_DATA/22566/DTI/MRI0/dti_ec_brain_mask.nii.gz"
> initialised with start = 95, strides = [ -1 96 9216 ]
> dwi2response [DEBUG]: image
> "/home/rr480/Code/KirstieDTI/SUB_DATA/22566/DTI/MRI0/dti_ec_brain_mask.nii.gz"
> unloaded
> dwi2response [DEBUG]: searching for suitable gradient encoding...
> dwi2response [INFO]: found 69x4 diffusion-weighted encoding
> dwi2response [INFO]: Diffusion gradient encoding data clustered into 2
> shells
> dwi2response [DEBUG]: loading image
> "/home/rr480/Code/KirstieDTI/SUB_DATA/22566/DTI/MRI0/dti_ec.nii.gz"...
> dwi2response: uncompressing image
> "/home/rr480/Code/KirstieDTI/SUB_DATA/22566/DTI/MRI0/dti_ec.nii.gz"... 100%
> dwi2response [DEBUG]: image
> "/home/rr480/Code/KirstieDTI/SUB_DATA/22566/DTI/MRI0/dti_ec.nii.gz" loaded
> dwi2response [DEBUG]: voxel accessor for image
> "/home/rr480/Code/KirstieDTI/SUB_DATA/22566/DTI/MRI0/dti_ec.nii.gz"
> initialised with start = 95, strides = [ -1 96 9216 645120 ]
> dwi2response: initialising response function...  100%
> dwi2response [INFO]: Initial response function is [331.3299255
> -81.32884216]
> dwi2response: optimising response function..  .    dwi2response [DEBUG]:
> voxel accessor for image
> "/home/rr480/Code/KirstieDTI/SUB_DATA/22566/DTI/MRI0/dti_ec.nii.gz"
> initialised with start = 95, strides = [ -1 96 9216 645120 ]
> dwi2response [DEBUG]: voxel accessor for image
> "/home/rr480/Code/KirstieDTI/SUB_DATA/22566/DTI/MRI0/dti_ec.nii.gz"
> initialised with start = 95, strides = [ -1 96 9216 ]
> dwi2response [DEBUG]: initialising threads...
> dwi2response [DEBUG]: launching 1 thread "run thread"...
> dwi2response [DEBUG]: launched thread "run thread" [ID 140638269503232]
> dwi2response [DEBUG]: waiting for completion of thread "run thread" [ID
> 140638269503232]...
> dwi2response [DEBUG]: failed to find SH peak!
> dwi2response [DEBUG]: failed to find SH peak!
> dwi2response [DEBUG]: failed to find SH peak!
> dwi2response [DEBUG]: failed to find SH peak!
> dwi2response [DEBUG]: failed to find SH peak!
> dwi2response [DEBUG]: failed to find SH peak!
> dwi2response [DEBUG]: failed to find SH peak!
> dwi2response [DEBUG]: failed to find SH peak!
> dwi2response [DEBUG]: failed to find SH peak!
> dwi2response [DEBUG]: failed to find SH peak!
> dwi2response [DEBUG]: failed to find SH peak!
> dwi2response [DEBUG]: failed to find SH peak!
> dwi2response [DEBUG]: failed to find SH peak!
> dwi2response [DEBUG]: failed to find SH peak!
> dwi2response [DEBUG]: failed to find SH peak!
> dwi2response [DEBUG]: failed to find SH peak!
> dwi2response [DEBUG]: failed to find SH peak!
> dwi2response [DEBUG]: failed to find SH peak!
> dwi2response [DEBUG]: failed to find SH peak!
> dwi2response [DEBUG]: failed to find SH peak!
> dwi2response [DEBUG]: failed to find SH peak!
> dwi2response [DEBUG]: failed to find SH peak!
> dwi2response [DEBUG]: failed to find SH peak!
>
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