Mrview: unknown option / unrecognized argument

1

Hi, all,

I meet two problems.

1).
When I type the command “mrview”, the output shows as below:

mrview HARDI150.mif -odf.load_sh HARDI150_fod.mif
mrview: unknown option “-odf.load_sh”

I used to use this command to check whether my odf image is right or not.

Then I checked mrtrix version:

$ mrconvert -version
== mrconvert 3.0_RC2-24-gfc18ca90 ==
64 bit release version, built Sep 4 2017, using Eigen 3.2.92
Author(s): J-Donald Tournier (jdtournier@gmail.com)
Copyright (c) 2008-2017 the MRtrix3 contributors.

2).

dwipreproc -rpe_none AP HARDI150_denoise.mif HARDI150_denoise_preproc.mif

the output shows:

Error: unrecognized arguments: HARDI150_denoise_preproc.mif
Usage: dwipreproc input output [ options ]
(Run dwipreproc -help for more information)

Can someone give some advice?

Thanks.
Chaoqing

2

  1. not sure what’s going on, but the first thing to do is verify that the version of mrview being invoked is actually the right one - you’re showing the output of mrconvert -version, try mrview -version to rule out any issues on that front. Otherwise I can’t see anything wrong with your command.

  2. dwipreproc now expects the phase-encode direction to be provided via the -pe_dir option (see help page for details). This change was introduced in version 3.0_RC1.

3

Hi, Donald,

The problem may not list here for laking -pe_dir option. Maybe I missed some tips.:
It seems that it can not recognize the output file:

dwipreproc -rpe_none AP DTI_30_average-6_denoise.mif -pe_dir j- DTI_30_average-6_denoise_preproc.mif

 Error: unrecognized arguments: DTI_30_average-6_denoise_preproc.mif
 Usage: dwipreproc input output [ options ]
       (Run dwipreproc -help for more information)

And, here is the information of the current data:

> mrinfo DTI_30_average-6.mif

************************************************
Image:               "DTI_30_average-6.mif"
************************************************
  Dimensions:        128 x 128 x 44 x 186
  Voxel size:        2 x 2 x 3 x ?
  Data strides:      [ -1 -2 3 4 ]
  Format:            MRtrix
  Data type:         unsigned 16 bit integer (little endian)
  Intensity scaling: offset = 0, multiplier = 1
  Transform:               0.9989    -0.03139     0.03407      -123.1
                          0.03463      0.9945    -0.09911      -107.2
                         -0.03077      0.1002      0.9945      -43.39
  EchoTime:          0.093
  PhaseEncodingDirection: j-
  TotalReadoutTime:  0.0531
  command_history:   mrconvert "DTI_30_average-6/" "DTI_30_average-6.mif"  (version=3.0_RC2-24-gfc18ca90)
  comments:          LIU YAN (8888) [MR] DTI_30_average-6
                     study: head Union Hospital [ ORIGINAL PRIMARY M ND MOSAIC ]
                     DOB: 13/11/1961
                     DOS: 13/11/2008 21:06:36
  dw_scheme:         0,0,0,0
  [186 entries]      0.20387258,0.52022557999999997,-0.82933800999999996,1000
                     ...
                     -0.85757386999999996,0.17731076000000001,0.48283326999999998,1000
                     -0.97915560000000001,0.17763335,0.098491999999999996,1000
  mrtrix_version:    3.0_RC2-24-gfc18ca90

Thanks,
Chaoqing

4

The problem is indeed with your usage as @jdtournier described:

dwipreproc -rpe_none AP DTI_30_average-6_denoise.mif -pe_dir j- DTI_30_average-6_denoise_preproc.mif

Here you are providing the phase-encoding direction twice: once as the first input argument “AP”, and again using the “-pe_dir j-” option.

If we strip away the command-line options, and only show the positional arguments, this is what your invocation looks like:

dwipreproc AP DTI_30_average-6_denoise.mif DTI_30_average-6_denoise_preproc.mif

That is, you have provided three arguments:

  1. “AP”
  2. “DTI_30_average-6_denoise.mif”
  3. “DTI_30_average-6_denoise_preproc.mif”

The command, however, expects two positional arguments:

Usage: dwipreproc input output

So the command thinks that “AP” is the input image, “DTI_30_average-6_denoise.mif” is the output image, and “DTI_30_average-6_denoise_preproc.mif” is … something that it doesn’t know what to do with. Unfortunately the error message is not as useful as it could be; but I can’t fix this without entirely removing the dependence of the MRtrix3 Python scripts on the argparse module and writing a command-line parser from scratch.

The misunderstanding also comes from the fact that the dwipreproc script used to require three arguments. In an earlier version, manually specifying the phase-encoding direction was not an optional parameter as it is now, but a compulsory command-line argument, which needed to appear before the path to the input file. So whatever is informing you to add “AP” to the start of the instruction is out-of-date.

Rob

5

Hi, Rob,

Thanks for your patience! The problem has been solved.

It is indeed my own fault, I should read the script more carefully.

Thanks,
Chaoqing