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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.
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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
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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')
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R Reynolds March, 2024
version 0.0
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