CONN manual & references

Software manual

CONN toolbox manual

Scripting in CONN

   Main user-facing scripting functions in CONN: 

>> conn_batch

create and manage all aspects of your functional connectivity projects using scripts 

>> conn_module

integrate modular CONN functions into your own preprocessing or analysis pipelines (e.g. for arbitrary / non-connectivity data)

see conn extensions for a description of all modules currently available in CONN: conn module PREP, conn module GLM, conn module EL, conn module FL

   Examples of use: see all "How to..." sections in fMRI Methods book

Compiling CONN

   If you have Matlab Compiler on your machine and CONN already installed, you may compile your own standalone version of CONN using the following commands:

>> cd(fullfile(fileparts(which('conn')),'standalone'));                    % cd to conn/standalone folder

>> if ismac, make_mac; elseif isunix, make_linux; else make_pc; end        % run OS-dependent make_* script  

   (note: default standalone versions for Linux/Mac/Windows are available at NITRC) 

Command-line utilities  (sorted by topic)

Command-line functions for file input/output/conversion:

>> conn_surf_read and conn_surf_write

reads/writes surface- level data (FreeSurfer fsaverage level-8 163K tessellation, with 163842 vertices and 327680 faces) from NIFTI format file

type "help conn_surf_write" in Matlab for additional details

e.g. :

>> conn_surf_write('data.surf.nii', rand([163842*2, 1]) ); % creates surface NIFTI file (e.g. 2 hemispheres 1 datapoint)

>> data = conn_surf_read('data.surf.nii'); % reads surface NIFTI file

>> conn_mtx_read and conn_mtx_write

reads/writes matrix-level data (arbitrary square matrix) from NIFTI format file

type "help conn_mtx_write" in Matlab for additional details

e.g. :

>> conn_mtx_write('data.mtx.nii', rand([10, 10, 1]) ); % creates matrix NIFTI file (e.g. 10 ROIs 1 datapoint)

>> data = conn_mtx_read('data.mtx.nii'); % reads matrix NIFTI file

>> conn_vol_read / conn_vol_write

reads/writes volume-level data (arbitrary 3D/4D matrix) from NIFTI format file

type "help conn_vol_write" in Matlab for additional details

e.g. :

>> conn_vol_write('data.nii', rand([64, 64, 64, 1]) ); % creates volume NIFTI file (e.g. single 3D image)

>> data = conn_vol_read('data.nii'); % reads volume NIFTI file

>> conn_dcm2nii : converts DICOM (.dcm ) to NIFTI format (.nii)

>> conn_gz2nii : converts compressed NIFTI (.gz ) to NIFTI format (.nii)

>> conn_matc2nii : converts CONN (.matc ) to NIFTI format (.nii)

>> conn_mgh2nii : converts MGH (.mgh .mgz ) to NIFTI format (.nii)

>> conn_annot2nii : converts FREESURFER annotation (lh*.annot rh*.annot) to surface NIFTI format (.surf.nii)

>> conn_surf_curv2nii : converts FREESURFER paint (lh. rh.) to surface NIFTI format (.surf.nii)

>> conn_surf_gii2nii : converts FREESURFER surface GIFTI (lh*.gii rh*.gii) to surface NIFTI format (.surf.nii)

>> conn_surf_nii2curv : converts surface NIFTI (.surf.nii) to FREESURFER paint format (lh. rh.)

>> conn_surf_nii2gii : converts surface NIFTI (.surf.nii) to FREESURFER surface GIFTI format (lh*.gii rh*.gii)

>> conn_cat2mgh : converts CAT12 output files to FREESURFER format

>> conn_surf_surf2vol :  projects surface NIFTI (.surf.nii) to volume NIFTI (.nii) format (in MNI-space)

>> conn_surf_vol2surf :  projects volume NIFTI (.nii) (in MNI-space) to surface NIFTI format (.surf.nii)

>> conn_cache pull/push

manages local cache (for fast repeated access to files stored in slow or remote drives)

type "help conn_cache" in Matlab for additional details

e.g. :

>> file = conn_cache('pull','/Volumes/ext/data.txt'); % creates local copy of remote/network file

>> edit(file); % change local copy

>> conn_cache('push','/Volumes/ext/data.txt'); % updates remote/network file with changes if necessary

Command-line functions for displaying data or results:

>> conn_display <SPM.mat>

displays group-level analysis results (including analyses of standard 3D volume-level data, as well as surface- and matrix-level analyses)

type "help conn_display" in Matlab for additional details

e.g. :

>> hf = conn_display('/results/analysis01/SPM.mat'); % displays 2nd-level analysis results

>> conn_display(hf, 'export_mask', 'mask.nii'); % exports supra-threshold mask

>> conn_mesh_display <file.nii>

displays MNI-space 3D volume or surface data projected onto a 3D cortical reference surface (Freesurfer tessellation of ICBM 2009c Nonlinear Asymmetric template)

type "help conn_mesh_display" in Matlab for additional details

e.g. :

>> fh = conn_mesh_display('/results/analysis01/spmT_0001.nii'); % displays T-stat map projected on cortical surface

>> fh('print', 4, 'figure01.jpg', '-nogui'); % prints 4-view mosaic

>> conn_slice_display <file.nii>

displays MNI-space 3D volume data overlaid on individual slices of a reference structural image (ICBM 2009c Nonlinear Asymmetric template)

type "help conn_slice_display" in Matlab for additional details

e.g. :

>> fh = conn_slice_display('/results/analysis01/spmT_0001.nii'); % displays T-stat map on individual slices

>> fh('pointer_mm',[0 0 10]); % sets display center coordinates to [0 0 10] mm

>> fh('multisliceset',true,16,8); % sets multi-slice display to 16 slices and 8mm interslice

>> fh('togglegui',true); % hide GUI buttons

>> fh('print', 'figure01.jpg', '-nogui'); % prints figure

>> conn_mtx_display <file.nii>

displays matrix-level data 

type "help conn_mtx_display" in Matlab for additional details

e.g. :

>> fh = conn_mtx_display('/results/analysis02/spmT_0001.nii'); % displays T-stat map from matrix group-analysis

>> fh('print', 'figure01.jpg', '-nogui'); % prints figure

>> conn_table_display (data)

displays contingency table data 

type "help conn_table_display" in Matlab for additional details

e.g. :

>> data = conn_roioverlaps( 'results.ROIs.nii', '/software/conn/rois/networks.nii'); % computes overlap between two groups of ROIs

>> fh = conn_table_display(a.overlap,'rlabel',a.rows_names,'clabel',a.cols_names); % displays table

>> fh('print', 'figure01.jpg', '-nogui'); % prints figure

Command-line functions to process/analyze arbitrary -non-connectivity- data:

>> conn module preprocessing <filename.json>

preprocesses and/or denoises arbitrary functional data. Processing methods include all those described in the Preprocessing pipeline and Denoising pipeline sections

type "help conn_module" in Matlab or see CONN module PREP for additional details

e.g. :

>> conn_module( 'preprocessing', 'PREPROC01.json' ); % runs default preprocessing pipeline on raw functional/structural data

example PREPROC01.json: (preprocessing only)

{

 "structurals": [ "/data/anat.nii" ],

 "functionals": [ [

   "/data/run1/func.nii",

   "/data/run2/func.nii"

  ] ],

 "steps": "default_mni",

 "sliceorder": "interleaved (Siemens)"

}

example PREPROC02.json: (preprocessing + denoising)

{

 "structurals": [ "/data/anat.nii" ],

 "functionals": [ [

   "/data/run1/func.nii",

   "/data/run2/func.nii"

  ] ],

 "steps": ["default_mni", "functional_regression", "functional_bandpass" ],

 "sliceorder": "interleaved (Siemens)",

 "reg_names": ["realignment", "scrubbing", "White Matter", "CSF"],

 "reg_dimensions": [Inf,Inf,5,5],

 "reg_deriv": [1,0,0,0],

 "bp_filter": [0.008,Inf]

}

>> conn module glm <filename.json>

performs group-level analyses of arbitrary data (including analyses of standard 3D volume-level data, as well as surface- and matrix-level analyses). Analyses methods include all those described in the Cluster-level inferences section (e.g. RFT, randomization/permutation, TFCE, NBS, etc.)

type "help conn_module" in Matlab or see CONN module GLM for additional details

e.g. :

>> conn_module( 'glm', 'ANALYSIS01.json'); % runs 2nd-level analysis of arbitrary input images

>> conn_display( '/results/analysis01' ); % displays results

example ANALYSIS01.json (defining a two-sample t-test with N=10):

{

 "data": [

  "/data/file01.nii",

  "/data/file02.nii",

  "/data/file03.nii",

  "/data/file04.nii",

  "/data/file05.nii",

  "/data/file06.nii",

  "/data/file07.nii",

  "/data/file08.nii",

  "/data/file09.nii",

  "/data/file10.nii"

 ],

 "design_matrix": [[1,0],[1,0],[1,0],[1,0],[1,0],[0,1],[0,1],[0,1],[0,1],[0,1]],

 "contrast_between": [-1,1],

 "contrast_within": 1,

 "folder": "/results/analysis01"

}

Command-line functions to submit or manage jobs in HPC/cluster environments:

>> conn_batch(..., 'parallel.N', N)

submits a request for N nodes in your cloud or HPC environment to execute the steps specified in a conn_batch command (each node will process/analyze a different subset of subjects)

type "help conn_batch" in Matlab for additional details

e.g.:

>> conn_batch('Denoising.done', true, 'parallel.profile', 'slurm', 'parallel.N', 10); 

% runs CONN denoising step on your current CONN project using 10 simultaneous

      % nodes/jobs, and using the Slurm protocol to submit these jobs

>> conn jobmanager 

manages jobs submitted to cloud or HPC environments

type "help conn_jobmanager" in Matlab for additional details

e.g.:

>> conn_jobmanager profiles % displays a list of all available HPC profiles

e.g.:

>> conn_jobmanager % launches gui displaying the status of any pending or running jobs

e.g.:

>> conn_jobmanager restartif error % restarts any nodes/jobs which have stopped with errors

>> conn('submit', fcn_name  [, arg1, arg2, ... ] )

 submits a request for a single node in your cloud or HPC environment to run the Matlab function or script fcn_name with (optional) input arguments arg1, arg2., etc.

e.g.:

>> conn submit myscript01; % run myscript01 remotely and wait until job finishes

e.g.:

>> job = conn('submit', 'myscript01'); % run myscript01 remotely and return immediately (before job starts)

>> conn_jobmanager('statusjob', job, [], true, true); % checks the status of a submitted job

>> conn submit_spmbatch <matlabbatch>

 submits arbitrary SPM batch <matlabbatch> (.m or .mat file, or matlabbatch structure) as a single job to your cloud or HPC environment

e.g.:

>> matlabbatch{1}.spm... = ... % define matlabbatch structure

>> save batchfile.mat matlabbatch;  % saves matlabbatch information in .mat file

>> conn submit_spmbatch batchfile.mat; % submit SPM batch file and wait until job finishes

Command-line functions to work with CONN remotely

>> conn remotely on

starts SSH-based encrypted/secure connection with remote server (this is not needed if you are already connected to a remote server in CONN's GUI)

e.g.:

>> conn remotely on

  Server address []: yourinstitution.edu

  Username []: 

  ...

>> conn_server cmd

runs interactive Matlab commands in remote CONN server

e.g.:

>> conn_server cmd % interactive command-line prompt (commands executed in CONN server)

 yourinstitution.edu >> vpa(pi,100) % run vpa function in remote CONN server

  ans =

  3.141592653589793238462643383279502884197169399375105820974944592307816406286208998628034825342117068

 yourinstitution.edu >> quit % exits interactive commands 

>> [out1, out2, ...] = conn_server('run', fcn_name, arg1, arg2, ... )

runs in remote CONN server the Matlab function or script fcn_name with (optional) input arguments arg1, arg2., etc.

e.g.:

>> out = conn_server('run', 'vpa', pi, 1000); run vpa function in remote CONN server and imports output variable

type "help conn_remotely"  in Matlab or see remote commands for additional functions