Friday, May 30, 2014

Automating 3dReHo

As a rider to our tale of Regional Homogeneity analysis, we last discuss here how to automate it over all the subjects of your neuroimaging fiefdom. Much of this will look similar to what we have done with other analyses, but in case you don't know where to start, this should help get you going.


setenv mask mask_group #Set your own mask here
setenv subjects "0050773 0050774" #Replace with your own subject numbers within quotations

foreach subj ($subjects)

cd {$subj}/session_1/{$subj}.results #Note that this path may be different for you; change accordingly

3dReHo -prefix ReHo_{$subj} -inset errts.{$subj}+tlrc -mask mask_group+tlrc #Perform Regional Homogeneity analysis

#Convert data to NIFTI format
3dAFNItoNIFTI ReHo_{$subj}+tlrc.HEAD
3dAFNItoNIFTI {$mask}+tlrc.HEAD

#Normalize images using FSL commands
setenv meanReHo `fslstats ReHo_{$subj}.nii -M`
setenv stdReHo `fslstats ReHo_{$subj}.nii -S`

fslmaths ReHo_{$subj}.nii -sub $meanReHo -div $stdReHo -mul mask_group.nii ReHo_Norm_{$subj}

gunzip *.gz

#Convert back to AFNI format
3dcopy ReHo_Norm_{$subj}.nii ReHo_Norm_{$subj}


1 comment:

  1. Will I get to see your videos on how to run resting state data using FSL? :)