Problems with dMRI_connectivity_advanced

[Johannes Bathelt]

Dear Nipy Users,

First of all thank you very much to the developers for providing such a useful and versatile package. I have been using the dMRI_connectivity_advanced (MRTrix version) script for a while now to obtain connectome measures. 

Unfortunately, the script stopped working two days ago - probably after installing updates to some Python modules. I'm now getting the following crash report from the probCSDstreamtrack node: 

Cannot set the undefined 'tracked.tck' attribute of a 'StreamlineTrackOutputSpec' object.

MRTrix itself and the command that is generated both run on my system so I suspect that it is some kind of permission error. NB: I'm using the Enthought Python distribution v. 2.7.6 under Mac OS 10.9.2. I tried different versions of NiPyPe (0.9.2 and latest developer version), but to no avail. I'd be grateful for any hints on how to resolve this issue. 

Thank you for your help

Joe

____________

Joe Bathelt, MSc

PhD candidate

Cognitive Neuroscience & Neuropsychiatry Section

UCL Institute of Child Health

[Erik Ziegler]

Hey,

I addressed this issue in a recent pull request, though it hasn't been merged yet. See https://github.com/nipy/nipype/pull/828

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[Chris Filo Gorgolewski]

Thanks Erik!

[Jozsef Kalinak]

Dear Nipy Users,

I'm new to Nipy, and I'm having trouble getting the dMRI_connectivity_advanced script to work. This is the error message:

File "dmri_connectivity_advanced.py", line 56, in <module>
    import nipype.interfaces.cmtk as cmtk
  File "/usr/local/lib/python2.7/dist-packages/nipype/interfaces/cmtk/__init__.py", line 3, in <module>
    from .parcellation import Parcellate
  File "/usr/local/lib/python2.7/dist-packages/nipype/interfaces/cmtk/parcellation.py", line 34, in <module>
    from cmp.util import runCmd
ImportError: No module named util

This is with the latest version of Connectome Mapper and Nipype. (and not with the forked version of Nipype the installation page of cmtk recommends)

Any help is appreciated

Jozsef

[Chris Filo Gorgolewski]

Hi,

What version of cmp are you using? Where did you obtain it? It look like API change on their side.

Best,

Chris

[Jozsef Kalinak]

Thank you for the suggestion, I used the 2.1.0-beta from http://www.cmtk.org/mapper/download.html

After I installed the the older version from https://github.com/LTS5/cmp the error message I'm getting is :

cmp_config = cmp.configuration.PipelineConfiguration()
AttributeError: 'module' object has no attribute 'configuration'


Is there a specific version of cmp I have to use?

Jozsef

[Erik Ziegler]

Yeah this is a very annoying problem.

At the moment my solution is to just checkout an old commit from CMP:

https://github.com/LTS5/cmp/commit/78608e986634341c1a0cb08ed0b7ea8a632307e3

using 

git checkout 78608e986634341c1a0cb08ed0b7ea8a632307e3

CC'd to cmtk-users in case someone there can help fix it. 

[John Griffiths]

praise the lord for version control!

[Erik Ziegler]

Hey,

That's a bit weird indeed. The parcellate interface definitely does have an ROI file output. See: http://www.mit.edu/~satra/nipype-nightly/interfaces/generated/nipype.interfaces.cmtk.parcellation.html

Perhaps you can clone and install Nipype from the master branch on github?

git clone https://github.com/nipy/nipype

cd nipype

python setup.py install

It looks like you're trying to clone it wrong:

First, clone the CMP repository:

git clone https://github.com/LTS5/cmp.git

then checkout the old commit:

git checkout 78608e986634341c1a0cb08ed0b7ea8a632307e3

Hope that helps!

P.s. To thank for the connectivity tutorial you can cite this paper (dx.doi.org/10.1371/journal.pone.0069290) in addition to the CMP and Nipype papers!

On Mon, Sep 8, 2014 at 6:18 PM, Alexis Hervais-Adelman <ag...@cantab.net> wrote:

Hi,
I am having the same (or a related) problem, whereby the dMRI_connectivity_advanced script fails because the latest version of CMP/CMTK is different than expected. I'll just pause tehre to say thank you for the script, and the associated comments, which are incredibly helpful.

I was able to circumvent the errors reported below by other users with some small modifications, but then when it comes to conecting the modules with:
mapping.connect([(parcellate, mri_convert_ROI_scale500,['roi_file','in_file')])])
it fails, retuning the error:
"Module Parcellate has no output called roi_file"
I am unable to clone the repository pointed to above, git fails with the following error: "fatal: https://github.com/LTS5/cmp/commit/78608e986634341c1a0cb08ed0b7ea8a632307e3/info/refs not valid: is this a git repository?
It would therefore be great to have a solution to this! Either to be able to get a copy of the modules that are compatible with thtis example, or just to have a bit info on what outputs Parcelalte does have.

Thanks in advance!

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