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Dear AFNI users-

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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

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xiyuezh
June 05, 2022 09:05PM
Hi experts,

After using afni_proc.py to preprocess some resting-state fMRI data, there are always some sub-bricks become zeros in the results. I tried several times and got the same results every run. For example, one of the 3dinfo infomation of one subject: 
3dinfo -verb errts.S126.tproject+tlrc.
Quote

......
-- At sub-brick #68 'S126.rs.02aptopu[68]' datum type is float: -48.3584 to 17.7858
-- At sub-brick #69 'S126.rs.02aptopu[69]' datum type is float: 0 to 0
-- At sub-brick #70 'S126.rs.02aptopu[70]' datum type is float: 0 to 0
-- At sub-brick #71 'S126.rs.02aptopu[71]' datum type is float: -19.4341 to 23.5937
......

my code 
afni_proc.py                                                 \
      -subj_id "$i"                                        \
      -dsets "$i".rs.02aptopup.nii.gz                            \
      -copy_anat "$i".T1.padded180.nii                                     \
      -blocks despike tshift align tlrc volreg blur mask scale regress  \
      -tcat_remove_first_trs 0                                  \
      -volreg_align_to MIN_OUTLIER                              \
      -volreg_align_e2a \
      -volreg_tlrc_warp \
      -mask_apply anat                                             \
      -mask_segment_anat yes                                      \
      -mask_segment_erode yes                                     \
      -blur_size 6                                              \
      -regress_censor_motion 0.5                               \
      -regress_censor_outliers 0.05                             \
      -regress_bandpass 0.01 0.1                                \
      -regress_apply_mot_types demean deriv                     \
      -regress_est_blur_epits                                   \
      -regress_est_blur_errts

Could you provide some advice? Thank you!


Xiyue



Edited 1 time(s). Last edit at 06/05/2022 09:05PM by xiyuezh.
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Subject Author Posted

afni_proc.py missing sub brick data

xiyuezh June 05, 2022 09:05PM

Re: afni_proc.py missing sub brick data

rick reynolds June 05, 2022 11:41PM