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LTS5 / cmp_nipype

This repository is meant to host a beta version for the future release of the ConnectomeMapper.
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bug in tracking.py - hardcoded curvature value #40

Open davegrays opened 8 years ago

davegrays commented 8 years ago

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 commented 8 years ago

@davidrs06 , can you have a look at this?

davidrs06 commented 8 years ago

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 commented 8 years ago

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 notifications@github.com 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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