Re: [HCP-Users] dMRI: Error while running "eddy_postproc.sh"

[Sang-Young Kim]

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  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"  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 
>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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> 
> 
> 
> 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.


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Re: [HCP-Users] dMRI: Error while running "eddy_postproc.sh"

[Harms, Michael]

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"  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 
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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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.

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[HCP-Users] dMRI: Error while running "eddy_postproc.sh"

[Sang-Young Kim]

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 
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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