Motion correcting Siemens moco series across scans.

AFNI Message Board
1

Hello,

If we are using the moco (motion corrected) series output from a Siemens 3T Trio, is it okay to still run motion correction on the images during preprocessing (i.e. 3dvolreg) or will this be introducing unnessary interpolation? Do the motion parameters from the moco series get accounted for in the motion output file from afni_proc.py? Would you recommend continuing to use the motion corrected images from the scanner or would it be better to use the original raw files and do all preprocessing post scanning session? We are combining multiple runs and currently use the following script (stim times/labes and glms removed for ease of reading):

afni_proc.py -subj_id $subj
-script proc.$subj -scr_overwrite
-out_dir ~/Desktop/Imaging/${study}_PDD/${subj}.PDD
-move_preproc_files
-blocks tshift despike align tlrc volreg blur mask scale regress
-copy_anat $anat_dir/$subj.MPRAGE+orig
-tcat_remove_first_trs 0
-dsets $epi_dir/${subj}.EPI?m+orig.HEAD
-align_opts_aea -giant_move
-volreg_align_to MIN_OUTLIER
-volreg_align_e2a
-volreg_tlrc_warp
-blur_size 4.0
-test_stim_files no
-regress_stim_times
-regress_stim_labels
-regress_local_times
-regress_basis ‘BLOCK5(1,1)’
-regress_stim_types
AM2 AM2 AM2 AM2 times AM2 AM2
-regress_opts_3dD
-jobs 5
-GOFORIT 5
-regress_reml_exec
-regress_opts_reml -GOFORIT
-regress_make_ideal_sum sum_ideal.1D
-regress_est_blur_epits
-regress_est_blur_errts

Any advice would be much appreciated as we cannot find very much information about what the Moco series is doing.

Thank you!

2

I prefer to use the non-corrected images for the reasons you ask. You cannot include exact motion regressors in your regression model if you use the MOCO. The fundamentals are mostly the same, but I prefer to trust in AFNI to do the heavy lifting. It’s easier to see exactly what the software is doing!

Your script looks mostly standard based on the examples that are provided in afni_proc.py. I usually only use the despike block in resting state data, and not in functional data.

3

I prefer to use the non-corrected series for data analysis for exactly the reason you point out. If you use the MOCO, it is not possible to include the exact motion parameters as regressors in your regression model.

Your script looks mostly standard. I usually only use the despike block in resting state analyses, and not in functional tasks.

4

Thank you Peter, this is very helpful! Do you have any suggestions for better processing MOCO series if that is all we have? For some of our older scans only the moco series was saved and we no longer have access to the original data.

Also, thank you for the information about despiking, it was never really clear to me if it should be used for functional tasks or not. We will take out the despike block in our analysis :slight_smile: