:orphan: .. _ahelp_ap_run_simple_rest_me.tcsh: ************************** ap_run_simple_rest_me.tcsh ************************** .. contents:: :local: | .. code-block:: none ------------------------------------------------------------------------------ ap_run_simple_rest_me.tcsh - run a quick afni_proc.py analysis for QC on multi-echo data usage: ap_run_simple_rest_me.tcsh [options] -anat ANAT -epi_me_run epi_run1_echo_*.nii ... This program is meant to run a moderately quick single subject analysis, treating the EPI as resting state data. Overview: 0. This program will change over time. Do not rely on a fixed version. See "ap_run_simple_rest_me.tcsh -ver" for the current version number. 1. Output files are placed in the current directory, so it is suggested to run from a "clean" location, generally away from the raw inputs. 2. Template registration is merely affine, to be fast. 3. By default, the first 2 time points are removed as pre-steady state. It is a good idea to set -nt_rm appropriately. inputs : anat (optional), EPI echos (one set of echoes per run), echo times controls : recommended opts: -subjid, -nt_rm outputs : run_ap_SUBJID - afni_proc.py command script : proc.SUBJID -_proc script (if AP is run) : SUBJID.results - proc results dir (if run) : out.* - text output files from AP and proc scripts This program may be devoured by afni_proc.py itself, at some point. ------------------------------------------------------------------------------ example 0: just create an afni_proc.py script, run_ap_SUBJ, no data required ap_run_simple_rest_me.tcsh -anat anat.nii -epi_me_run epi_echo_*.nii -echo_times 20 30 40 example 1: quickly process EPI (no anat, so no align/tlrc blocks) ap_run_simple_rest_me.tcsh -epi_me_run epi_echo_*.nii -echo_times 20 30 40 example 2: run an analysis from a clean directory We should really not run from a data source directory, but it is done to keep paths short. The test.ap directory can be removed once run. cd APMULTI_Demo1_rest/data_00_basic/sub-005/ses-01 mkdir test.ap cd test.ap ap_run_simple_rest_me.tcsh \ -subjid sub-005 \ -anat ../anat/sub-*_mprage_run-1_T1w.nii.gz \ -epi_me_run ../func/sub-*_task-rest_run-1_echo-*_bold.nii.gz \ -echo_times 12.5 27.6 42.7 \ -nt_rm 4 \ -run_proc example 3: similar to 2, but assuming there are 4 runs, 3 echoes in each ap_run_simple_rest_me.tcsh \ -subjid sub-005 \ -epi_me_run ../func/sub-*_task-rest_run-1_echo-*_bold.nii.gz \ -epi_me_run ../func/sub-*_task-rest_run-2_echo-*_bold.nii.gz \ -epi_me_run ../func/sub-*_task-rest_run-3_echo-*_bold.nii.gz \ -epi_me_run ../func/sub-*_task-rest_run-4_echo-*_bold.nii.gz \ -echo_times 12.5 27.6 42.7 \ -nt_rm 4 \ -run_proc ------------------------------------------------------------------------------ terminal options: -help : show this help -hist : show the program history -ver : show the version number required parameters: -epi_me_run EPI_echo_1 EPI_echo_2 ... : specify one run of EPI echo dsets example: -epi_me_run epi_run-1_echo-*.nii.gz example: -epi_me_run epi_run-1_echo-*.nii.gz -epi_me_run epi_run-2_echo-*.nii.gz -epi_me_run epi_run-3_echo-*.nii.gz -epi_me_run epi_run-4_echo-*.nii.gz This option specifies the EPI data, but each such option specifies one run of all echoes. If there are 5 runs, then 5 such option sets should be used. -echo_times e1_time e2_time e3_time ... : specify echo times, in ms example: -echo_times 12.5 27.6 42.7 optional parameters: -anat ANAT : specify single anatomical dataset This is used for anat/EPI alignment, as well as anat/template alignment. -nt_rm NT : num time points to remove from starts of runs def: 2 -run_ap : actually run the afni_proc.py command def: do not, just generate AP command script -run_proc : do the processing (run the proc script from AP) def: do not run AP or proc script -subjid SUBJ_ID : specify subject ID for file names def: SUBJ -template TEMPLATE : specify template for standard space def: MNI152_2009_template_SSW.nii.gz -compressor COMP : control automatic compression of *.BRIK files. 'COMP' must be one of the allowed keywords for the AFNI_COMPRESSOR environment variable: GZIP COMPRESS BZIP2 PIGZ and you must have the associated program for compression installed (e.g., 'gzip') def: not set here -verb VERB : specify verbosity level (3 == -echo) def: 1 -echo : set 'echo' in the shell, as if run via 'tcsh -x' (same as '-verb 3') ------------------------------------------------------------------------------ R Reynolds March, 2024 version 0.0 ------------------------------------------------------------------------------