afni.nimh.nih.gov

Hi!
I am a total newbe with afni and I struggle with a rather simple thing regarding data quality control. The @ss_review scripts are not working after afni completed afni_proc.py. Any help would be appreciated since the easy data quality check is one of the things that I really like about afni.

I use the following simple loop to run the preprocessing and first level analysis for each participant (vp). The ouput of ss_review_basic and ss_review_driver can be found below.

Thank you in advance!

Johannes

#!/usr/bin/env tcsh

# created by uber_subject.py: version 0.37 (April 14, 2015)
# creation date: Thu Jul 30 18:07:19 2015

# set data directories vp03 vp04 bereits gelaufen

foreach vpid   ( vp02 vp05 vp06 vp07 vp08 vp09 vp10 vp11 vp12 vp13 vp14 vp15 vp16 vp17 )
set top_dir   = /Users/fMRI/Documents/Subitizing_Gestalt
set anat_dir  = $top_dir/$vpid/DICOM
set epi_dir   = $top_dir/$vpid/DICOM
set stim_dir  = $top_dir/Timings_Gestalt_10TRs

# set subject and group identifiers
set subj      = $vpid
set group_id  = all

# run afni_proc.py to create a single subject processing script
afni_proc.py -subj_id $subj                                                     
        -script proc.$subj -scr_overwrite                                      
        -blocks tshift align tlrc volreg blur mask scale regress     
        -copy_anat $anat_dir/anat+orig                                        
        -tcat_remove_first_trs 10                                            
        -dsets $epi_dir/gestalt+orig.HEAD                               
        -align_opts_aea -giant_move                                     
        -tlrc_base MNI_avg152T1+tlrc                                    
        -volreg_align_to MIN_OUTLIER                                    
        -volreg_align_e2a                                               
        -volreg_tlrc_warp                                               
        -blur_size 5.0                                                  
        -regress_stim_times                                             
            $stim_dir/${vpid}_gestalt_t.txt                             
            $stim_dir/${vpid}_no_gestalt_t.txt                          
        -regress_stim_labels                                            
            gestalt_t no_gestalt_t                                      
        -regress_basis 'GAM'                                            
        -regress_censor_motion 0.3                                      
        -regress_censor_outliers 0.1                                    
        -regress_apply_mot_types demean deriv                           
        -regress_opts_3dD                                               
            -jobs 2                                                     
            -gltsym 'SYM: gestalt_t -no_gestalt_t' -glt_label 1 G-N     
            -gltsym 'SYM: 0.5*gestalt_t +0.5*no_gestalt_t' -glt_label 2 
        mean.GN                                                         \
            -gltsym 'SYM: no_gestalt_t -gestalt_t' -glt_label 3 N-G     
            -gltsym 'SYM: gestalt_t' -glt_label 4 G                     
            -gltsym 'SYM: no_gestalt_t' -glt_label 5 N                  
        -regress_reml_exec                                              
        -regress_make_ideal_sum sum_ideal.1D                            
        -regress_est_blur_epits                                         
        -regress_est_blur_errts

tcsh -xef proc.$vpid |& tee output.proc.$vpid

end

-----------------------------------

# Output of @ss_review

fMRI% /Users/fMRI/Documents/Gestalt_1st_level/vp05.results/@ss_review_basic ; exit;

subject ID : vp05
TRs removed (per run) : 10
num stim classes provided : 2
final anatomy dset : anat_final.vp05+tlrc.HEAD
final stats dset : stats.vp05+tlrc.HEAD
final voxel resolution : NO-DSET NO-DSET NO-DSET

motion limit : 0.3
** Can't read time series file motion_vp05_enorm.1D
num TRs above mot limit : 0
average motion (per TR) : ** Program compile date = Jul 17 2015
** Can't read time series file motion_vp05_enorm.1D
average censored motion : ** Program compile date = Jul 17 2015
max motion displacement :
max censored displacement :
outlier limit : 0.1
average outlier frac (TR) : ** Program compile date = Jul 17 2015
** Can't read time series file outcount_rall.1D
num TRs above out limit : 0

num runs found : failed to open 1D file X.xmat.1D ** failed to read text data file X.xmat.1D
num TRs per run : failed to open 1D file X.xmat.1D ** failed to read text data file X.xmat.1D
num TRs per run (applied) : failed to open 1D file X.xmat.1D ** failed to read text data file X.xmat.1D
num TRs per run (censored): failed to open 1D file X.xmat.1D ** failed to read text data file X.xmat.1D
fraction censored per run : failed to open 1D file X.xmat.1D ** failed to read text data file X.xmat.1D
rows_cols: Subscript out of range.
logout

------------------------------

# output of ss_review_driver


*** missing @ss_review_basic script ***

------------------- outliers and motion --------------------
[1] 10525
[2] 10526
++ 1dplot: AFNI version=AFNI_2011_12_21_1014 (Jul 17 2015) [64-bit]
++ Authored by: RWC et al.
++ 1dplot: AFNI version=AFNI_2011_12_21_1014 (Jul 17 2015) [64-bit]
++ Authored by: RWC et al.
[3] 10527
++ 1dplot: AFNI version=AFNI_2011_12_21_1014 (Jul 17 2015) [64-bit]
++ Authored by: RWC et al.
** FATAL ERROR: can't read -censor file 'censor_vp05_combined_2.1D'
** Program compile date = Jul 17 2015
** FATAL ERROR: can't read -censor file 'censor_vp05_combined_2.1D'
** Program compile date = Jul 17 2015
** FATAL ERROR: can't read -censor file 'censor_vp05_combined_2.1D'
** Program compile date = Jul 17 2015]



Edited 1 time(s). Last edit at 07/31/2015 06:05AM by Johannes_Tuebingen.