Beginner for Mrtrix3

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Hi, Donald,

I try to use ACT followed the instruction of "http://community.mrtrix.org/t/beginner-connectome-pipeline-updated/373 "My commands are as follows:

  1. I run dwidenoise command:
    $ dwidenoise DTI/ DTI_denoise.mif

  2. I generate the DTI.mif file as well as DTI.bvecs and DTI.bvals files with the command:
    $ mrconvert DTI_denoise.mif DTI_denoise_convert.mif -export_grad_fsl DTI_denoise_convert.bvecs DTI_denoise_convert.bvals

  3. I run dwipreproc command:
    $ dwipreproc -rpe_none 2 DTI_denoise_convert.mif DTI_denoise_convert_preproc.mif

After the 3th step, the output is:

dwipreproc: 
dwipreproc: Note that this script makes use of commands / algorithms that have relevant articles for citation; INCLUDING FROM EXTERNAL SOFTWARE PACKAGES. Please consult the help page (-help option) for more information.
dwipreproc: 
dwipreproc: Generated temporary directory: /tmp/dwipreproc-tmp-M88GP6/
Command: mrconvert /media/windows-share/DTI_denoise_convert.mif /tmp/dwipreproc-tmp-M88GP6/series.mif
dwipreproc: Changing to temporary directory (/tmp/dwipreproc-tmp-M88GP6/)
Command: mrconvert series.mif dwi_pre_topup.nii -stride -1,+2,+3,+4
dwipreproc: Creating phase-encoding configuration file
Command: dwi2mask series.mif - | maskfilter - dilate - | mrconvert - mask.nii -datatype float32 -stride -1,+2,+3
Command: mrconvert series.mif - -stride -1,+2,+3,+4 | mrinfo - -export_grad_fsl bvecs bvals
Command: eddy --imain=dwi_pre_topup.nii --mask=mask.nii --index=indices.txt --acqp=config.txt --bvecs=bvecs --bvals=bvals --out=dwi_post_eddy

Then, it just stopped here, without any error and output.
After half an hour, It still in this status and I have to cancel this command with the output:

^CTraceback (most recent call last):
  File "/home/brain/mrtrix3/scripts/dwipreproc", line 317, in <module>
    runCommand(eddy_cmd + ' --imain=' + eddy_in + ' --mask=mask.nii --index=indices.txt --acqp=config.txt --bvecs=bvecs --bvals=bvals' + eddy_in_topup + ' --out=dwi_post_eddy')
  File "/home/brain/mrtrix3/scripts/lib/runCommand.py", line 104, in runCommand
    (stdoutdata, stderrdata) = process.communicate()
  File "/usr/lib/python2.7/subprocess.py", line 799, in communicate
    return self._communicate(input)
  File "/usr/lib/python2.7/subprocess.py", line 1409, in _communicate
    stdout, stderr = self._communicate_with_poll(input)
  File "/usr/lib/python2.7/subprocess.py", line 1463, in _communicate_with_poll
    ready = poller.poll()
KeyboardInterrupt

And also, I don’t know the PE direction is 2 or not, and I tried different values, however the results are the same.
oh, right, my mrinfo is as follows. Probably, we cannot find the PE direction here, but I think it is necessary to show it:

************************************************
Image:               "DTI_30_average-2_denoise.mif"
************************************************
  Dimensions:        128 x 128 x 44 x 62
  Voxel size:        2 x 2 x 3 x ?
  Data strides:      [ -2 -3 4 1 ]
  Format:            MRtrix
  Data type:         32 bit float (little endian)
  Intensity scaling: offset = 0, multiplier = 1
  Transform:                0.999   5.447e-08     0.04556      -128.9
                          0.00254      0.9984    -0.05571      -112.4
                         -0.04549     0.05576      0.9974         -43
  comments:          zhou (090726cont) [MR] DTI_30_average-2
                     study: head Union Hospital
                     DOB: 26/07/1995
                     DOS: 26/07/2009 13:12:41
  dw_scheme:         [ 62 entries ]
  mrtrix_version:    0.3.15-266-g2bf78387

I don’t know how it happened. It seems that I interrupt the process. Really? If so, the process is too slow…
Do you have any ideas?

thnaks,
Chaoqing