Getting Started with CANLab fMRI Data Preprocessing

Check SPM Defaults

Tor advises that you should change the following default settings in spm_defaults.m

edit spm_defaults

  • defaults.stats.maxmem = 2^33; %modified from 2^26
  • defaults.mask.thresh = -Inf; %modified from 0.8
  • defaults.stats.fmri.hpf = 180; %modified from 128
  • defaults.stats.fmri.cvi = 'None'; %modified from 'AR(1)'

Follow the appropriate file structure

Note: some path structures are hard coded, so try not to change things once you start analyzing. To avoid headaches, do not name your project folder similarly to existing project folders.

Correct for signal stabilization

Discard roughly the first 5 TRs at the start of each run to allow for signal stabilization. The number of discarded volumes should be informed by the scanner you recorded data from.

It is recommended to do this before preprocessing, using fsl.

Example function: disdaqs.sh

#!/bin/bash
    
FIN=${1%.nii}
TRIM=${2:-5}
DIR=$(dirname $FIN)
FIN=$(basename $FIN)
    
cd $DIR
    
fslsplit $FIN -t
rm $FIN.nii
mkdir disdaqs
mv $(ls vol* | head -$TRIM) disdaqs
fslmerge -t $FIN vol*
rm vol*
fslchfiletype NIFTI $FIN
    
exit 0

Preprocessing Scripts

There are two main preprocessing scripts: preproc_part1 and preproc_part2 which are a part of canlab_preproc. Click on procedure to see the series of steps

Data Quality Checks

When you are done preprocessing, review the data quality. see this page for more on preproc's output

help/fmri_help/preprocessing/a_start_here.txt · Last modified: 2016/08/19 18:00 (external edit)
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