Removing last TRs in only one run

AFNI Message Board
1

Hello, I am trying to remove the last 10 TRs in one of 6 runs and I keep receiving an error when I use the command -tcat_remove_last_trs 0 0 0 10 0 0\ to do so. The error says this: ** error: option -tshifts_opts_ts follows unknown arg #34 (10). Is there another way to remove only the last few TRs for one run during preprocessing? Below is my preprocessing script.

afni_proc.py -subj_id DASHH_7 -verb 2 -script
DASHH_7_preproc_results_ginormous.tcsh -out_dir 7/results -dsets
7/func/7_bold_checker_11+orig.HEAD
7/func/7_bold_checker_15+orig.HEAD
7/func/7_bold_asset_17+orig.HEAD
7/func/7_bold_asset_18+orig.HEAD
7/func/7_bold_asset_20+orig.HEAD
7/func/7_bold_asset_21+orig.HEAD -anat_has_skull no -copy_anat
7/anat/7_MPRAGE_masked4+orig.HEAD -blocks despike tshift align tlrc
volreg blur mask scale regress -tcat_remove_first_trs 4
-tcat_remove_last_trs 0 0 0 10 0 0
-tshift_opts_ts -tpattern alt+z2
-align_opts_aea -save_epi_ns -check_flip -AddEdge -ginormous_move
-tlrc_base
/data/nil-bluearc/hershey/unix/DASHH/DASHH_FMRI_2/MNI152_T1_2009c+tlrc.HEAD
-tlrc_NL_warp -volreg_align_to first
-volreg_interp -heptic
-volreg_opts_vr
-maxdisp1D
-volreg_align_e2a -volreg_tlrc_warp
-blur_in_automask
-blur_size 8.0
-regress_censor_motion 0.5

2

The -tcat_remove_first_trs and -tcat_remove_last_trs options remove a constant number of time points from the start and end of each run.

In order to remove some from just one run, you will have to do that before running afni_proc.py. e.g.,

3dTcat -prefix run3.drop.last.2 run3+orig'[0..197]'
  • rick
3

Got it, thank you.

4

I just happened to come back to this. My mistake, the first TRs can vary across runs, but not the last.

If it is still useful, I will make these symmetric and allow for both to vary.

Sorry about that.

  • rick