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205 days ago
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Unfiled. Edited by Marianne Reddan 205 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/

205 days ago
0 / 19
Unfiled. Edited 205 days ago
yoniashar@gmail.com ** NOTE: if you use MRN's auto-analysis, it does all of the below for you! **
Motivation: to understand the components of the data you collected and how to prepare them for preprocessing
 
  • You will have to move the script to that folder. A copy of it is in CANLabRepos/trunk/Misc/Dream-specific also it can be found in ruzic/scripts or in other experiment folders
  • on blanca, this script is at /data/projects/wagerlab/git/Repository/CanlabPrivate/Misc/Dream-specific
  • on blanca, this script is at /data/projects/wagerlab/git/Repository/CanlabPrivate/Misc/Dream-specific
 
Tor has preferences for the SPM defaults which will influence preprocessing & analysis, so update the spm_defaults.m file accordingly: Remember not to edit the file directly -- see the documentation at the top of the file.
 
506 days ago
Unfiled. Edited by Adam Teed 506 days ago
  • spm8_timing_correction
 
952 days ago
Unfiled. Edited by Marianne Reddan 952 days ago
preproc_part2
Marianne R 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 
  • cellstr of subjects' mean prewarped functional images
  • Optional PREPROC2 fields:
  • .inplane_files 
  • cellstr of subjects' T1 images with the same number of slices as a functional image, but much higher resolution within the slice - useful as an intermediate image, but not required
  • .templ 
  • canonical image to warp to - (default: avg152T1.nii);
  • .spm_ver
  • 'SPM2' or 'SPM5' - (default: SPM8)
  • Other parameters
  • wh_subjs 
  • vector of numbers indicating which subjects to preprocess (default: all subjects)
  • set_origins 
  • set origins of images (default: 1)
  • warp 
  • set normalization of functional images (default: 1)
  • smooth 
  • set smoothing of functional images (default: 1)
  • check_norms 
  • check the fitness of the normalization (default: 0) this is better run separately, after all preprocessing is done
  • coreg anat to func 
  • coregister the anatomical image too the mean func (default: 1)
  • don't turn this off unless you know for a fact they're already coregistered; if in doubt, leave on
  • generate mean 
  • generate mean wra img (default: 1)
  • meaningless if warping result images (e.g., con*nii, spmT*nii, beta*nii, etc)
 
 
Members (44)
Bogdan Petre Marianne Reddan Mark Labinski Daniel Weflen marta ceko Hedwig Adam Teed Nikhil Mahendra Stephan Geuter Martin Lindquist Neda Kaboodvand Shaun Eack Tor Wager Daniel Lee eehitchcock@gmail.com stephan.geuter@colorado.edu Feng Zhou brooke.carter@colorado.edu gordon.matthewson@gmail.com anjali.krishnan@colorado.edu
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