Human Connectome Project subject list

[syoh]

Hello, Thanks for working on this much needed software.

I am having trouble processing the Human Connectome Data with CPAC. What I am trying to achieve is the nuisance signal regression. http://fcp-indi.github.io/docs/user/nuisance.html

I tried using the following subject list:

anatomicalTemplate  :  /home/yoohoo/Data/%s/%s/T1w.nii.gz 
functionalTemplate  :  /home/yoohoo/Data/%s/%s/MNINonLinear/Results/rfMRI_REST*_LR/rfMRI_REST*_*_hp2000_clean.nii.gz 
subjectList  :  None 
exclusionSubjectList  :  None 
siteList  :  None 
scanParametersCSV  :  None 
outputSubjectListLocation  :  /home/yoohoo/Data/hcp_output 

I get the following error:

In [2]: CPAC.utils.extract_data.run('data_config.yaml')
For any errors or messages check the log file - /home/syoh/Data/extract_data_logs.log
---------------------------------------------------------------------------
Exception                                 Traceback (most recent call last)
/home/syoh/Data/<ipython-input-2-855581fc0eb7> in <module>()
----> 1 CPAC.utils.extract_data.run('data_config.yaml')

/usr/local/lib/python2.7/dist-packages/CPAC/utils/extract_data.pyc in run(data_config)
    518         s_param_map = None
    519 
--> 520     extract_data(c, s_param_map)
    521     generate_suplimentary_files(c.outputSubjectListLocation)
    522 

/usr/local/lib/python2.7/dist-packages/CPAC/utils/extract_data.pyc in extract_data(c, param_map)
    206 
    207     func_session_present, func_session_path, func_relative = \
--> 208         check_for_sessions(func_relative, func_relative_len)
    209 
    210     anat_session_present, anat_session_path, anat_relative = \

/usr/local/lib/python2.7/dist-packages/CPAC/utils/extract_data.pyc in check_for_sessions(relative_path, path_length)
    202                   "For more information refer to manual"
    203             logging.exception(msg)
--> 204             raise Exception(msg)
    205         return session_present, session_path, relative_path
    206 

Exception: extract_data script currently doesn't support this directory structure.Please provide the subjects_list file to run CPAC.For more information refer to manual

Am I doing something wrong? Thanks for your help!

[stymy]

Hi Syoh,

Thanks for using CPAC.

Could you tell me what the actual directory paths are to your data? Where is an example rest and anatomical file located?

-Aimi

[syoh]

Hi stymy,

Thanks for getting back to me.

I decided to use the preprocessed files that the human connectome project (HCP) releases in order to skip many of the steps. All I want to do with CPAC is global signal regression.

What is the best way to make CPAC just do this portion of the pipeline? Would this be possible?

[stymy]

Every CPAC function has an on/off selection, so it should be possible to just run global signal regression.

From the pipeline configuration window you open Environment Setup > Preprocessing Workflow Options and turn off gather/run anatomical analysis and keep on gather/run functional data preprocessing. Likewise, turn off other functional preprocessing functions that you do not wish to perform.

In order to select global signal regression, navigate to Nuisance > Nuisance Correction and add a new option under Corrections using the green (+) button. Then check off global.

I hope this helps!