AFNI Message Board

Dear AFNI users-

We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:

https://discuss.afni.nimh.nih.gov

Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.

The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.

Sincerely, AFNI HQ

History of AFNI updates  

Previous Message Next Message
Message List New Topic Print View
|
Nshin96
July 15, 2019 02:27AM
Thank you so much for the simple explanation!

For now, I have edited my afni_proc.py based on example 9b: resting state analysis with ANATICOR, as follows: 

afni_proc.py -subj_id $subj                                        \
        -script proc.$subj -scr_overwrite                          \
        -blocks despike tshift align tlrc volreg blur mask regress \
        -copy_anat $top_dir/anat_shft.nii                          \
        -dsets $top_dir/run1_shft+orig.HEAD                        \
        -tcat_remove_first_trs 3                                   \
        -align_opts_aea -giant_move                                \
        -tlrc_base MNI_avg152T1+tlrc                               \
        -tlrc_opts_at -OK_maxite                                   \
        -volreg_align_to MIN_OUTLIER                               \
        -volreg_align_e2a                                          \
        -volreg_tlrc_warp                                          \
        -blur_size 4.0                                             \
        -mask_epi_anat yes                                         \
        -regress_anaticor                                          \
        -regress_censor_motion 0.2                                 \
        -regress_bandpass 0.01 0.1                                 \
        -regress_apply_mot_types demean deriv                      \
        -regress_motion_per_run                                    \
        -regress_est_blur_errts                                    \
        -regress_run_clustsim no

However, I face another problem.. now I am encountering an error with 3dDeconvolve. 

++ 3dDeconvolve extending num_stimts from 0 to 118 due to -ortvec
++ 3dDeconvolve: AFNI version=AFNI_19.1.23 (Jun 24 2019) [64-bit]
++ Authored by: B. Douglas Ward, et al.
++ STAT automask has 74515 voxels (out of 271633 = 27.4%)
++ Skipping check for initial transients
++ Input polort=4; Longest run=492.5 s; Recommended minimum polort=4 ++ OK ++
++ Number of time points: 197 (before censor) ; 42 (after)
 + Number of parameters:  123 [123 baseline ; 0 signal]
** ERROR:  *** Censoring has made regression impossible :( ***
** FATAL ERROR: 3dDeconvolve dies: Insufficient data (42) for estimating 123 parameters

It appears that there are too many time points being censored (looking at the motion_censor.1D file, there does seem to be quite a bit of motion in fMRI, so I suppose that makes sense), but I am not sure why there are so many parameters for resting fMRI. Where would I go from here?
Reply Quote
RSS
Subject Author Posted

3dAllineate Fatal Error - @Align_Center?

Nshin96 July 11, 2019 09:26PM

Re: 3dAllineate Fatal Error - @Align_Center?

ptaylor July 12, 2019 08:50AM

Re: 3dAllineate Fatal Error - @Align_Center?

Nshin96 July 15, 2019 02:27AM

Re: 3dAllineate Fatal Error - @Align_Center?

ptaylor July 15, 2019 08:23AM

Re: 3dAllineate Fatal Error - @Align_Center?

Nshin96 July 15, 2019 09:07PM

Re: 3dAllineate Fatal Error - @Align_Center?

ptaylor July 15, 2019 09:59PM