Hi Gang,
This is my first time to use ICA tool to process resting state fMRI data. Would you please take a look at the steps I have taken to see whether there is any problem? I am not quite sure whether the pre-processing steps are correct. The other thing is after 3dICA.R how I can create AFNI activation map for each of the components.
Thanks,
Iris
P.S.
#pre-processing raw EPI of a single subject
3dTshift -prefix ts_RestEyeClose+orig RestEyeClose+orig
3dvolreg -dfile mot_tempRestEyeClose -base 'ts_RestEyeClose+orig[163]' -prefix reg_RestEyeClose ts_RestEyeClose+orig
3dmerge -1blur_fwhm 4 -doall -prefix reg_RestEyeClose_blur reg_RestEyeClose+orig
3dcalc -prefix RestEyeClose_mask800 -a 'ts_RestEyeClose+orig[163]' -expr 'astep(a,800)'
#Pre-processing for ICA analysis: dimensionality reduction
3dpc -quiet -mask RestEyeClose_mask800+orig -reduce 10 redim_RestEyeClose -prefix PreICA_RestEyeClose reg_RestEyeClose_blur+orig
adwarp -apar T1Volume+tlrc -dpar 'redim_RestEyeClose+orig' -dxyz 3 -prefix ICAInput_RestEyeClose_dxyz3
# find the components
3dICA.R RestEyeClose_dxyz3_ICAOutput
par.txt file is as below.
Input:ICAInput_RestEyeClose_dxyz3+tlrc
CompOutput: RestEyeClose_dxyz3_ICAOutput
MixOutput:Temp
NoComp:10
Func:logcosh
Type:parallel
