Re: [HCP-Users] Problem with gradunwarp

2018-11-16 Thread Anthony Dick 
Hello Matt,

Thanks for the response. Taylor Salo (CC’d) forked it from the Wash U version 
to make it more Python 3 compatible and to fix a couple of bugs (see 
https://github.com/FIU-Neuro/gradunwarp/pull/1). However, we are still 
encountering this same issue. Hopefully it is an easy fix!

Anthony

--
Anthony Steven Dick, Ph.D.
Associate Professor
Director, Cognitive Neuroscience Program and Graduate Certificate in Cognitive 
Neuroscience
Florida International University MM Campus AHC4 454
Department of Psychology and Center for Children and 
Families<http://www.ccf.fiu.edu/>, an FIU Preeminent 
Program<https://beyondpossible.fiu.edu/preeminent-programs/>
11200 S.W. 8th Street
Miami, FL 33199
Ph: 305-348-4202; Lab Ph: 305-348-9055; Fx: 305-348-3879
Email: ad...@fiu.edu<mailto:ad...@fiu.edu>; Webpage: 
http://dcn.fiu.edu<http://dcn.fiu.edu/>; Join the 
SSHD<http://www.sshdonline.org/>
#
Check out the new book<http://www.routledge.com/9781138960039>:
Dick, A.S., & Müller, U. (2018). Advancing Developmental Science: Philosophy, 
Theory, and Method. Taylor & Francis.


From: "Glasser, Matthew" 
Date: Thursday, November 15, 2018 at 7:07 PM
To: Anthony Dick , "hcp-users@humanconnectome.org" 

Subject: Re: [HCP-Users] Problem with gradunwarp

Is this the latest version of gradunwarp?  What python are you using?

Matt.

From: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Anthony Dick mailto:ad...@fiu.edu>>
Date: Thursday, November 15, 2018 at 8:49 AM
To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] Problem with gradunwarp

Hello!

We have been trying to use gradunwarp on Siemens Prisma diffusion data (we’re 
using: 
https://github.com/Washington-University/gradunwarp<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_Washington-2DUniversity_gradunwarp=DwMF-g=lhMMI368wojMYNABHh1gQQ=DmdQWjwCJRFVHJCqLOrjwA=VcXEbpZNXlIIoHl1-5wpKVkbHYQ0o_uAhmq0CBssJ60=5UsjrVI0vSSkoOBGMFptSDm5UxLi8HmHzOb_RYCGse8=>).

We have encountered what appears to be the same problem as described here: 
https://www.mail-archive.com/hcp-users@humanconnectome.org/msg01679.html<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.mail-2Darchive.com_hcp-2Dusers-40humanconnectome.org_msg01679.html=DwMF-g=lhMMI368wojMYNABHh1gQQ=DmdQWjwCJRFVHJCqLOrjwA=VcXEbpZNXlIIoHl1-5wpKVkbHYQ0o_uAhmq0CBssJ60=ui7STi5oHPMLLRN-JDYKFOHC60ZyEHlysYd5BzYuSyc=>

However, it is not clear how this was resolved (an email to the poster suggests 
it may not have been). We’re looking for either a solution to this issue, or 
suggestions for alternative programs to achieve the same goal (preferably not 
matlab).

Here is a complete screen-dump of the error:

(/home/data/nbc/data-analysis/env3) -bash-4.1$ gradient_unwarp.py 
/home/data/dcnlab/AHEAD/sub-4150318/ses-S1/dwi/sub-4150318_ses-S1_run-01_dwi.nii.gz
 
/home/data/dcnlab/AHEAD/sub-4150318/ses-S1/dwi/sub-4150318_ses-S1_run-01_desc-unwarp_dwi.nii.gz
 siemens -g /home/data/dcnlab/AHEAD/coeff.grad -n
gradunwarp-INFO: Parsing /home/data/dcnlab/AHEAD/coeff.grad for harmonics coeffs
gradunwarp-INFO: Evaluating spherical harmonics
gradunwarp-INFO: on a 60^3 grid
gradunwarp-INFO: with extents -300.0mm to 300.0mm
gradunwarp-INFO: along x...
gradunwarp-INFO: along y...
gradunwarp-INFO: along z...
gradunwarp-INFO: Evaluating the jacobian multiplier
gradunwarp-INFO: Unwarping slice by slice
. Traceback (most recent call last):
  File "/home/data/nbc/data-analysis/env3/bin/gradient_unwarp.py", line 122, in 

grad_unwarp.run()
  File "/home/data/nbc/data-analysis/env3/bin/gradient_unwarp.py", line 111, in 
run
self.unwarper.run()
  File 
"/home/data/nbc/data-analysis/env3/lib/python3.6/site-packages/gradunwarp/core/unwarp_resample.py",
 line 154, in run
m_rcs2lai, m_rcs2lai_nohalf, g_xyz2rcs)
  File 
"/home/data/nbc/data-analysis/env3/lib/python3.6/site-packages/gradunwarp/core/unwarp_resample.py",
 line 274, in non_linear_unwarp_siemens
order=self.order)
  File 
"/home/data/nbc/data-analysis/env3/lib/python3.6/site-packages/scipy/ndimage/interpolation.py",
 line 319, in map_coordinates
raise RuntimeError('invalid shape for coordinate array')
RuntimeError: invalid shape for coordinate array
(/home/data/nbc/data-analysis/env3) -bash-4.1$

Thanks for any help,

Anthony

--
Anthony Steven Dick, Ph.D.
Associate Professor
Director, Cognitive Neuroscience Program and Graduate Certificate in Cognitive 
Neuroscience
Florida International University MM Campus AHC4 454
Department of Psychology and Center for Children and 
Families<http://www.ccf.fiu.edu/>, an FIU Preeminent 
Program<https://beyondpossible.fiu.edu/preeminent-programs/>
11200 S.W. 8th Street
Miami, FL 33199
Ph: 305-348-4202; Lab Ph: 305-348-9055; Fx: 305-348-3879
Email: ad

Re: [HCP-Users] Problem with gradunwarp

2018-11-15 Thread Glasser, Matthew 
I believe the current version of the Wash U version works with Python 2 and 
supports Prisma gradient tables.  If you aren’t using that version, it might 
not work.  I don’t write python so I don’t maintain gradunwarp.

Matt.

From: Anthony Dick mailto:ad...@fiu.edu>>
Date: Thursday, November 15, 2018 at 7:06 PM
To: Matt Glasser mailto:glass...@wustl.edu>>, 
"hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
mailto:hcp-users@humanconnectome.org>>
Cc: Taylor Salo mailto:tsalo...@fiu.edu>>
Subject: Re: [HCP-Users] Problem with gradunwarp

Hello Matt,

Thanks for the response. Taylor Salo (CC’d) forked it from the Wash U version 
to make it more Python 3 compatible and to fix a couple of bugs (see 
https://github.com/FIU-Neuro/gradunwarp/pull/1). However, we are still 
encountering this same issue. Hopefully it is an easy fix!

Anthony

--
Anthony Steven Dick, Ph.D.
Associate Professor
Director, Cognitive Neuroscience Program and Graduate Certificate in Cognitive 
Neuroscience
Florida International University MM Campus AHC4 454
Department of Psychology and Center for Children and 
Families<http://www.ccf.fiu.edu/>, an FIU Preeminent 
Program<https://beyondpossible.fiu.edu/preeminent-programs/>
11200 S.W. 8th Street
Miami, FL 33199
Ph: 305-348-4202; Lab Ph: 305-348-9055; Fx: 305-348-3879
Email: ad...@fiu.edu<mailto:ad...@fiu.edu>; Webpage: 
http://dcn.fiu.edu<http://dcn.fiu.edu/>; Join the 
SSHD<http://www.sshdonline.org/>
#
Check out the new book<http://www.routledge.com/9781138960039>:
Dick, A.S., & Müller, U. (2018). Advancing Developmental Science: Philosophy, 
Theory, and Method. Taylor & Francis.


From: "Glasser, Matthew" mailto:glass...@wustl.edu>>
Date: Thursday, November 15, 2018 at 7:07 PM
To: Anthony Dick mailto:ad...@fiu.edu>>, 
"hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] Problem with gradunwarp

Is this the latest version of gradunwarp?  What python are you using?

Matt.

From: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Anthony Dick mailto:ad...@fiu.edu>>
Date: Thursday, November 15, 2018 at 8:49 AM
To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] Problem with gradunwarp

Hello!

We have been trying to use gradunwarp on Siemens Prisma diffusion data (we’re 
using: 
https://github.com/Washington-University/gradunwarp<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_Washington-2DUniversity_gradunwarp=DwMF-g=lhMMI368wojMYNABHh1gQQ=DmdQWjwCJRFVHJCqLOrjwA=VcXEbpZNXlIIoHl1-5wpKVkbHYQ0o_uAhmq0CBssJ60=5UsjrVI0vSSkoOBGMFptSDm5UxLi8HmHzOb_RYCGse8=>).

We have encountered what appears to be the same problem as described here: 
https://www.mail-archive.com/hcp-users@humanconnectome.org/msg01679.html<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.mail-2Darchive.com_hcp-2Dusers-40humanconnectome.org_msg01679.html=DwMF-g=lhMMI368wojMYNABHh1gQQ=DmdQWjwCJRFVHJCqLOrjwA=VcXEbpZNXlIIoHl1-5wpKVkbHYQ0o_uAhmq0CBssJ60=ui7STi5oHPMLLRN-JDYKFOHC60ZyEHlysYd5BzYuSyc=>

However, it is not clear how this was resolved (an email to the poster suggests 
it may not have been). We’re looking for either a solution to this issue, or 
suggestions for alternative programs to achieve the same goal (preferably not 
matlab).

Here is a complete screen-dump of the error:

(/home/data/nbc/data-analysis/env3) -bash-4.1$ gradient_unwarp.py 
/home/data/dcnlab/AHEAD/sub-4150318/ses-S1/dwi/sub-4150318_ses-S1_run-01_dwi.nii.gz
 
/home/data/dcnlab/AHEAD/sub-4150318/ses-S1/dwi/sub-4150318_ses-S1_run-01_desc-unwarp_dwi.nii.gz
 siemens -g /home/data/dcnlab/AHEAD/coeff.grad -n
gradunwarp-INFO: Parsing /home/data/dcnlab/AHEAD/coeff.grad for harmonics coeffs
gradunwarp-INFO: Evaluating spherical harmonics
gradunwarp-INFO: on a 60^3 grid
gradunwarp-INFO: with extents -300.0mm to 300.0mm
gradunwarp-INFO: along x...
gradunwarp-INFO: along y...
gradunwarp-INFO: along z...
gradunwarp-INFO: Evaluating the jacobian multiplier
gradunwarp-INFO: Unwarping slice by slice
. Traceback (most recent call last):
  File "/home/data/nbc/data-analysis/env3/bin/gradient_unwarp.py", line 122, in 

grad_unwarp.run()
  File "/home/data/nbc/data-analysis/env3/bin/gradient_unwarp.py", line 111, in 
run
self.unwarper.run()
  File 
"/home/data/nbc/data-analysis/env3/lib/python3.6/site-packages/gradunwarp/core/unwarp_resample.py",
 line 154, in run
m_rcs2lai, m_rcs2lai_nohalf, g_xyz2rcs)
  File 
"/home/data/nbc/data-analysis/env3/lib/python3.6/site-packages/gradunwarp/core/unwarp_resample.py",
 line 274, in non_linear_unwarp_siemens
order=self.order)
  File 
"/home/data/nbc/data-analysis/env3/lib/python3.6/si

Re: [HCP-Users] Problem with gradunwarp

2018-11-15 Thread Glasser, Matthew 
Is this the latest version of gradunwarp?  What python are you using?

Matt.

From: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Anthony Dick mailto:ad...@fiu.edu>>
Date: Thursday, November 15, 2018 at 8:49 AM
To: "hcp-users@humanconnectome.org" 
mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] Problem with gradunwarp

Hello!

We have been trying to use gradunwarp on Siemens Prisma diffusion data (we’re 
using: https://github.com/Washington-University/gradunwarp).

We have encountered what appears to be the same problem as described here: 
https://www.mail-archive.com/hcp-users@humanconnectome.org/msg01679.html

However, it is not clear how this was resolved (an email to the poster suggests 
it may not have been). We’re looking for either a solution to this issue, or 
suggestions for alternative programs to achieve the same goal (preferably not 
matlab).

Here is a complete screen-dump of the error:

(/home/data/nbc/data-analysis/env3) -bash-4.1$ gradient_unwarp.py 
/home/data/dcnlab/AHEAD/sub-4150318/ses-S1/dwi/sub-4150318_ses-S1_run-01_dwi.nii.gz
 
/home/data/dcnlab/AHEAD/sub-4150318/ses-S1/dwi/sub-4150318_ses-S1_run-01_desc-unwarp_dwi.nii.gz
 siemens -g /home/data/dcnlab/AHEAD/coeff.grad -n
gradunwarp-INFO: Parsing /home/data/dcnlab/AHEAD/coeff.grad for harmonics coeffs
gradunwarp-INFO: Evaluating spherical harmonics
gradunwarp-INFO: on a 60^3 grid
gradunwarp-INFO: with extents -300.0mm to 300.0mm
gradunwarp-INFO: along x...
gradunwarp-INFO: along y...
gradunwarp-INFO: along z...
gradunwarp-INFO: Evaluating the jacobian multiplier
gradunwarp-INFO: Unwarping slice by slice
. Traceback (most recent call last):
  File "/home/data/nbc/data-analysis/env3/bin/gradient_unwarp.py", line 122, in 

grad_unwarp.run()
  File "/home/data/nbc/data-analysis/env3/bin/gradient_unwarp.py", line 111, in 
run
self.unwarper.run()
  File 
"/home/data/nbc/data-analysis/env3/lib/python3.6/site-packages/gradunwarp/core/unwarp_resample.py",
 line 154, in run
m_rcs2lai, m_rcs2lai_nohalf, g_xyz2rcs)
  File 
"/home/data/nbc/data-analysis/env3/lib/python3.6/site-packages/gradunwarp/core/unwarp_resample.py",
 line 274, in non_linear_unwarp_siemens
order=self.order)
  File 
"/home/data/nbc/data-analysis/env3/lib/python3.6/site-packages/scipy/ndimage/interpolation.py",
 line 319, in map_coordinates
raise RuntimeError('invalid shape for coordinate array')
RuntimeError: invalid shape for coordinate array
(/home/data/nbc/data-analysis/env3) -bash-4.1$

Thanks for any help,

Anthony

--
Anthony Steven Dick, Ph.D.
Associate Professor
Director, Cognitive Neuroscience Program and Graduate Certificate in Cognitive 
Neuroscience
Florida International University MM Campus AHC4 454
Department of Psychology and Center for Children and 
Families, an FIU Preeminent 
Program
11200 S.W. 8th Street
Miami, FL 33199
Ph: 305-348-4202; Lab Ph: 305-348-9055; Fx: 305-348-3879
Email: ad...@fiu.edu; Webpage: 
http://dcn.fiu.edu; Join the 
SSHD
#
Check out the new book:
Dick, A.S., & Müller, U. (2018). Advancing Developmental Science: Philosophy, 
Theory, and Method. Taylor & Francis.


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