Hi Gang,

I tried to do group ICA. Using the method proposed by Calhoun et al. (2004), I reduced each subject's time points from 164 to 64 using PCA and then concatenated all subjects into one dataset. I used combined dataset to be the input of 3dICA.R.

However, I had alignment problem. The concatenated functional run did not align with anatomical run well. I also tried convert all the functional run in to tlrc and then concatenate, but it did not work.

Did I do something wrong? I've attached the script I wrote in the end. Do you have any recommendation about how to do group ICA?

I would greatly appreciate your help.

Thanks,
Iris

P.S
# reduce time points for each subject from 164 to 41 using PCA

3dpc -vmean -vnorm -pcsave 30 -float -mask RestEyeClose_mask800+orig -prefix PreICA_timepoint40_{$sub} reg_RestEyeClose_blur+orig

#concatenate data from all subjects

3dTcat -session . -prefix PreICA_concat_before_dimreduce_8Ss PreICA_timepoint40_RS_001+orig PreICA_timepoint40_RS_002+orig PreICA_timepoint40_RS_003+orig PreICA_timepoint40_RS_005+orig PreICA_timepoint40_RS_008+orig PreICA_timepoint40_RS_009+orig PreICA_timepoint40_RS_010+orig PreICA_timepoint40_RS_014+orig

#reduce dimension of aggregated data to 20 (number of sources selected)
3dpc -mask RestEyeClose_mask800+orig -reduce 20 PreICA_concat_redim_RestEyeClose -prefix PreICA_RestEyeClose PreICA_concat_before_dimreduce_8Ss+orig

#tlrc aggregated data
adwarp -apar T1Volume+tlrc -dpar 'PreICA_concat_redim_RestEyeClose+orig' -dxyz 3 -prefix ICAInput_RestEyeClose_dxyz3

# find the components
# .gz file can not be processed, needs to be unziped

gunzip ICAInput_RestEyeClose_dxyz3+tlrc.BRIK.gz

3dICA.R RestEyeClose_dxyz3_ICAOutput