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59 days ago
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Unfiled. Edited by Marianne Reddan 59 days ago
Mission: To provide a guide that holds your hand through all the steps of CANLab data analyses, and provides a brief theoretical motivation for each step. 
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This document is maintained by Marianne Reddan.
Contact: marianne.reddan@colorado.edu
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For more information on this software check out http://canlabcore.readthedocs.org/
359 days ago
Unfiled. Edited by Adam Teed 359 days ago
A detailed look at step one of the CANLab preprocessing script.
  • Inputs & Outputs
  • [preprocessed_files mean_image_name] = preproc_part1(PREPROC,  ['slice timing', 0|1], ['motion correction', 0|1], ['local', 0|1], ['verbose', 0|1], ['clean_up', 0|1], ['save plots', 0|1], ['SPM2' | 'SPM5'], ['movie', 0|1], ['mean func', 0|1], ['run_dir_base', subpath])
Inputs
  • Required
  • PREPROC
  • a structure containing:
  • .func_files 
  • a cellstr of Nifti .nii or Analyze .img files containing the data
  • .TR
806 days ago
Unfiled. Edited by Marianne Reddan 806 days ago
Goal: Performs co-registration, normalization, and smoothing. It takes images from realignment (ravols) to smoothed, normalized functions (swravols).
  • Inputs & Outputs
  • preproc_part2(PREPROC2, ['set_origins', 0|1], ['warp', 0|1], ['smooth', 0|1], ['check norms', 0|1], ['SPM2' | 'SPM5'], ['wh_subjs', n], ['coreg anat to func', 0|1], ['generate mean', 0|1], ['verbose', 0|1], ['clean up', 0|1], ['save plots', 0|1])
Inputs
  • PREPROC2 is a structure containing these fields:
  • .anat_files 
  • cellstr of subjects' anatomical images
  • .files_to_warp  
  • cell array of cellstrs of subjects' functional images or result images (also falls back to .ra_func_files)
  • .mean_ra_func_files 
808 days ago
Unfiled. Edited by Marianne Reddan 808 days ago
  • OVERVIEW
  • canlab_glm_* are a set of functions to handle the running
  • of glm analyses of fmri data. They use SPM for analysis of
  • individual subjects and Tor Wager's robust regression
  • functions (robfit) for group level analysis. Details can
  • be found in the description of the DSGN structure (below) 
  • and in the help statements for the functions, but here is a brief
  • overview:
  •  
  • Before running canlab_glm functions, you will need to have:
808 days ago
Unfiled. Edited by Marianne Reddan 808 days ago
  • %DSGN STRUCTURE
  • %This is the structure variable used by canlab_glm_subject_levels to define an analysis.
  • %(note: optional fields/fields with defaults may be left undefined)
  •  
  •  ________________________________________________________________________________
  • | DSGN.metadata                                     |
  • |   a fieldname for the user to use as desired (typically for annotation).     |
  • |   EX: DSGN.metadata.notes = 'this design uses a modified HRF from model 4';     |
  • |________________________________________________________________________________|
  •  ________________________________________________________________________________
808 days ago
Unfiled. Edited by Marianne Reddan 808 days ago
  •  
  • %% AN EXAMPLE OF SETTING UP THE DSGN STRUCT FOR canlab_glm_subject_levels
  • % WARNING: none of these values are to be taken as recommendations!
  • % (to make executable, this would be saved as an M-file)
  •  
  • % All of the options below that are set to false here need not be included 
  • % (they default to false) but have been included in this example simply 
  • % as a reminder that they exist.
  •  
  • DSGN.metadata.notes = 'this is just an example DSGN setup in case you want to see how Luka set up his DSGN struct';

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