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  

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August 16, 2019 12:47PM
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
Subject Author Posted

Removing last TRs in only one run

emarler August 16, 2019 12:47PM

Re: Removing last TRs in only one run

rick reynolds August 16, 2019 01:52PM

Re: Removing last TRs in only one run

emarler August 19, 2019 05:30PM

Re: Removing last TRs in only one run

rick reynolds August 26, 2019 02:13PM