Analysing Openfmri data - Coregistration failure!

AFNI Message Board
1

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

2

Try adding the following to your script:


-align_opts_aea -giant_move
3

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
4

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