bug in tracking.py - hardcoded curvature value

[davegrays]

Running CMP from commandline, the value for is not recognized from the .ini file. Instead it appears to be hardocded depending on whether you run probabilistic or deterministic tractography.

If I comment out the _SD_changed() and _tracking_mode_changed() methods in cmp_nipype/cmp/stages/diffusion/tracking.py (lines 66 and 74), that fixes the problem. But assuming these are intended to provide default values in the GUI, I'm guessing there's a better solution. There's also a similar looking method for the Camino_tracking_config - I don't know if that will pose a similar problem.

[daducci]

@davidrs06 , can you have a look at this?

[davidrs06]

Hello davegrays ! Could you provide more details on how you are using the CMP from commandline ? If I create a config file and set the mrtrix tracking curvature to be 3.0 (as opposed to the 2.0 default value) and run the following code inside python:
import cmp.gui
project = cmp.gui.CMP_Project_Info()
project.base_directory = '/my/base/directory'
project.config_file = '/my/diffusion/config.ini'
pipeline = cmp.project.init_project(project, False)
valid_inputs = pipeline.check_input(gui=False)
print(pipeline.stages['Diffusion'].config.mrtrix_tracking_config.curvature)

The returned value is 3.0, as specified in the config file.

[davegrays]

Hi David,

I am just running 'connectomemapper subjectID config.ini' from the linux
command prompt, where I have set the mrtrix curvature to 1 or 3 in the
config.ini. In either case it runs streamtrack with a curvature value of 2.

-David

On Mon, Apr 4, 2016 at 2:41 AM, David Romascano [email protected]
wrote:

Hello davegrays ! Could you provide more details on how you are using the
CMP from commandline ? If I create a config file and set the mrtrix
tracking curvature to be 3.0 (as opposed to the 2.0 default value) and run
the following code inside python:
import cmp.gui
project = cmp.gui.CMP_Project_Info()
project.base_directory = '/my/base/directory'
project.config_file = '/my/diffusion/config.ini'
pipeline = cmp.project.init_project(project, False)
valid_inputs = pipeline.check_input(gui=False)
print(pipeline.stages['Diffusion'].config.mrtrix_tracking_config.curvature)

The returned value is 3.0, as specified in the config file.

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