Hello,
As part of a project we are trying to analyse the OpenfMRI ds000001 (R 2.0.4) dataset which is freely available here:
https://openfmri.org/dataset/ds000001/
However, checking our subject-level analyses with the @ss_review_driver command our coregistration between the anat and EPI image is off for all subjects. Here is the script generated by uber_subject.py that we are using to the run the first subjects analysis:
#!/usr/bin/env tcsh
created by uber_subject.py: version 0.39 (March 21, 2016)
creation date: Tue Sep 13 15:59:22 2016
run afni_proc.py to create a single subject processing script
afni_proc.py -subj_id sub01
-script proc.sub01 -scr_overwrite
-blocks tshift align tlrc volreg blur mask scale regress
-copy_anat /Users/cmaumet/Projects/Data_sharing/dev/Software_Comparison/ds001/AFNI/PREPROCESSING/ANATOMICAL/sub-01_T1w.nii
-tcat_remove_first_trs 2
-dsets
/Users/cmaumet/Projects/Data_sharing/dev/Software_Comparison/ds001/AFNI/PREPROCESSING/FUNCTIONAL/sub-01_task-balloonanalogrisktask_run-01_bold.nii.gz
/Users/cmaumet/Projects/Data_sharing/dev/Software_Comparison/ds001/AFNI/PREPROCESSING/FUNCTIONAL/sub-01_task-balloonanalogrisktask_run-02_bold.nii.gz
/Users/cmaumet/Projects/Data_sharing/dev/Software_Comparison/ds001/AFNI/PREPROCESSING/FUNCTIONAL/sub-01_task-balloonanalogrisktask_run-03_bold.nii.gz
-volreg_align_to third
-volreg_align_e2a
-volreg_tlrc_warp
-blur_size 5.0
-regress_stim_times
/Users/cmaumet/Projects/Data_sharing/dev/Software_Comparison/ds001/AFNI/ONSETS/sub-01_combined_cash_demean_afni.1d
/Users/cmaumet/Projects/Data_sharing/dev/Software_Comparison/ds001/AFNI/ONSETS/sub-01_combined_cash_RT_afni.1d
/Users/cmaumet/Projects/Data_sharing/dev/Software_Comparison/ds001/AFNI/ONSETS/sub-01_combined_control_pumps_demean_afni.1d
/Users/cmaumet/Projects/Data_sharing/dev/Software_Comparison/ds001/AFNI/ONSETS/sub-01_combined_control_pumps_RT_afni.1d
/Users/cmaumet/Projects/Data_sharing/dev/Software_Comparison/ds001/AFNI/ONSETS/sub-01_combined_explode_demean_afni.1d
/Users/cmaumet/Projects/Data_sharing/dev/Software_Comparison/ds001/AFNI/ONSETS/sub-01_combined_pumps_demean_afni.1d
/Users/cmaumet/Projects/Data_sharing/dev/Software_Comparison/ds001/AFNI/ONSETS/sub-01_combined_pumps_RT_afni.1d
-regress_stim_labels
cash_demean cash_RT control_pumps_demean
control_pumps_RT explode_demean pumps_demean
pumps_RT
-regress_basis_multi
‘BLOCK(0.772,1)’ ‘dmBLOCK’ ‘BLOCK(0.772,1)’ ‘dmBLOCK’
‘BLOCK(0.772,1)’ ‘BLOCK(0.772,1)’ ‘dmBLOCK’
-regress_stim_types
AM2 AM1 AM2 AM1 AM2 AM2 AM1
-regress_censor_motion 0.3
-regress_opts_3dD
-gltsym ‘SYM: pumps_demean -control_pumps_demean’
-glt_label 1 pumps_demean_vs_ctrl_demean
-regress_make_ideal_sum sum_ideal.1D
-regress_est_blur_epits \
Any advice would be greatly appreciated - we are slightly mystified at the moment as we ran similar analyses for another OpenfMRI dataset earlier this year and our results were great!
Alex