help > trouble with conn_module
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Jun 4, 2024  01:06 PM | Arianna Menardi
trouble with conn_module

Dear Experts,


 


I'm trying to run the following code that was posted on the CONN website:


conn_module('preprocessing',...


             'functionals',   {'/data/my_func.nii'}, ...


             'covariates',    struct(...


                 'names',     {{'realignment','scrubbing'}},...


                 'files',     {{'/data/moco.par', '/data/art_regression_outliers.mat'}}),...


             'masks',         struct(...


                 'White',     {{'/data/WM.nii'}},...


                 'CSF',       {{'/data/CSF.nii'}}), ...


             'steps',         {'functional_regression', 'functional_bandpass'}, ...


             'reg_names',     {'realignment','scrubbing','White Matter','CSF'}, ...


             'reg_dimensions',[inf, inf, 5, 5], ...


             'reg_deriv',     [1, 0, 0, 0], ...


             'bp_filter',     [0.008 inf] )


I  already have preprocessed my data (outside conn) and I only want to run the denoising part.


 


HOWEVER, if I run the code I get this error in matlab:


CONN: RUNNING SETUP.PREPROCESSING STEP
Error using conn_setup_preproc
unrecognized option covariates


Error in conn_process (line 27)
            case 'setup_preprocessing', conn_disp(['CONN: RUNNING SETUP.PREPROCESSING STEP']); conn_setup_preproc(varargin{:});


Error in conn_batch (line 1099)
            conn_process('setup_preprocessing',steps,'subjects',SUBJECTS,OPTIONS{:});


Error in conn_module (line 319)
        conn_batch(Batch);


Error in my_conn (line 50)
    conn_module('Preprocessing', ...


 


can you help me understand what is wrong?


 


Thank you

Jun 4, 2024  03:06 PM | Alfonso Nieto-Castanon - Boston University
RE: trouble with conn_module

Dear Arianna,


I think this may be just the result of an incompatibility of that conn_module syntax with a relatively older version of CONN, could you please try updating CONN to the latest release and then trying this syntax again?


Best


Alfonso


Originally posted by Arianna Menardi:



Dear Experts,


 


I'm trying to run the following code that was posted on the CONN website:


conn_module('preprocessing',...


             'functionals',   {'/data/my_func.nii'}, ...


             'covariates',    struct(...


                 'names',     {{'realignment','scrubbing'}},...


                 'files',     {{'/data/moco.par', '/data/art_regression_outliers.mat'}}),...


             'masks',         struct(...


                 'White',     {{'/data/WM.nii'}},...


                 'CSF',       {{'/data/CSF.nii'}}), ...


             'steps',         {'functional_regression', 'functional_bandpass'}, ...


             'reg_names',     {'realignment','scrubbing','White Matter','CSF'}, ...


             'reg_dimensions',[inf, inf, 5, 5], ...


             'reg_deriv',     [1, 0, 0, 0], ...


             'bp_filter',     [0.008 inf] )


I  already have preprocessed my data (outside conn) and I only want to run the denoising part.


 


HOWEVER, if I run the code I get this error in matlab:


CONN: RUNNING SETUP.PREPROCESSING STEP
Error using conn_setup_preproc
unrecognized option covariates


Error in conn_process (line 27)
            case 'setup_preprocessing', conn_disp(['CONN: RUNNING SETUP.PREPROCESSING STEP']); conn_setup_preproc(varargin{:});


Error in conn_batch (line 1099)
            conn_process('setup_preprocessing',steps,'subjects',SUBJECTS,OPTIONS{:});


Error in conn_module (line 319)
        conn_batch(Batch);


Error in my_conn (line 50)
    conn_module('Preprocessing', ...


 


can you help me understand what is wrong?


 


Thank you