Analysing Openfmri data - Coregistration failure!

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

Try adding the following to your script:


-align_opts_aea -giant_move

Many of those datasets had invalid NIFTI headers. So
worse than them being far enough off to require -giant_move
or maybe @Align_Centers, some might even be viewed as
left/right flipped.

So if alignment fails again, consider running @Align_Centers
on each dataset with the template as the -base dataset.

Also, consider expanding Peter’s option to include a test
for being left/right flipped:

-align_opts_aea -giant_move -check_flip
  • rick

Also consider using “-ginormous_move” on those problematic datasets.