Oh, I see. Yes, the —combrain-data-flag in DiffPreprocPipeline.sh was 1 since I
did not touch it.
I will try to use "2".
Thank you so much.
Sang-Young
> On Aug 25, 2017, at 12:30 PM, Harms, Michael <mha...@wustl.edu> wrote:
>
>
> See the --combine-data-flag in DiffPreprocPipeline.sh
> The default value of 1 is intended for acquisitions in which you have
> acquired the full vector table with both polarities, which isn’t how you
> acquired your data.
> In your case, you’ll need to use a value of ‘2’ for that flag.
>
> Cheers,
> -MH
>
> --
> Michael Harms, Ph.D.
>
> -----------------------------------------------------------
> Conte Center for the Neuroscience of Mental Disorders
> Washington University School of Medicine
> Department of Psychiatry, Box 8134
> 660 South Euclid Ave.Tel: 314-747-6173
> St. Louis, MO 63110Email: mha...@wustl.edu
>
> On 8/25/17, 11:23 AM, "hcp-users-boun...@humanconnectome.org on behalf of
> Sang-Young Kim" <hcp-users-boun...@humanconnectome.org on behalf of
> sykim...@gmail.com> wrote:
>
> Dear HCP users:
>
> I have another problem for running Diffusion Preprocessing pipeline. After
> eddy current correction, the pipeline proceeded to run eddy_postproc.sh. But
> I got error message as follow:
>
> **********************************************************
> Traceback (most recent call last):
> File "/Users/sang-young/projects/Pipelines/global/scripts/average_bvecs.py",
> line 296, in <module>
> overlap2)
> File "/Users/sang-young/projects/Pipelines/global/scripts/average_bvecs.py",
> line 36, in main
> bvals1 = loadFile(bvals1file, 1, [-1])
> File "/Users/sang-young/projects/Pipelines/global/scripts/average_bvecs.py",
> line 127, in loadFile
> raise ValueError('Wrong number of dimensions: {0}'.format(filename))
> ValueError: Wrong number of dimensions:
> /Volumes/LaCieMac3TB/HIV_HCP_pipeline/Data/30067/Diffusion/eddy/Pos.bval
> **************************************************************
>
> Above message came up while running the command (see below) in
> "eddy_postproc.sh".
> *********************************************************************
> ${globalscriptsdir}/average_bvecs.py ${eddydir}/Pos.bval
> ${eddydir}/Pos_rotated.bvec ${eddydir}/Neg.bval ${eddydir}/Neg_rotated.bvec
> ${datadir}/avg_data ${eddydir}/Pos_SeriesVolNum.txt
> ${eddydir}/Neg_SeriesVolNum.txt
> *********************************************************************
>
> Our dMRI data has been acquired with diffusion direction of 113 (AP
> direction) and b0 image were acquired with opposite direction (e.g., PA) for
> topup. So I have 1x113 bval and 3x113 bvec for DWI AP data, and 1x1 bval
> (e.g., 0 value) and 3x1 bvec (also 0 values) for DWI PA data.
>
> Something is wrong in bval and/or bvec file?
>
> It will be greatly appreciated if you can help me.
>
> Thanks in advance.
>
> Sang-Young Kim, Ph.D.
>
> Postdoctoral Research Fellow
> Department of Radiology, University of Pittsburgh
>
>
>
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