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
_______________________________________________
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users
________________________________
The materials in this message are private and may contain Protected Healthcare
Information or other information of a sensitive nature. If you are not the
intended recipient, be advised that any unauthorized use, disclosure, copying
or the taking of any action in reliance on the contents of this information is
strictly prohibited. If you have received this email in error, please
immediately notify the sender via telephone or return mail.
_______________________________________________
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users
