Hello,
As part of a project we are trying to analyse the OpenfMRI ds000001 (R 2.0.4) dataset which is freely available here:
[
openfmri.org]
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
