# -----------------------------------------------------------------------
This program is for building a selector string for AFNI subbricks
and/or 1D text files. It makes use of J. Rajendra's
'@djunct_dwi_selector.tcsh' script to make a list of 'bad' volume
indices by clicking on individual volumes in a montage image. Pretty
cool.
In the end, a selector string of volumes *to keep* (i.e., the
complement of the set of indices chosen with clicks) is output to
screen as well as stored in a text file.
Ver. 1.7 (PA Taylor, Feb 12, 2019)
# ----------------------------------------------------------------------
OUTPUT:
+ PPP_bads.txt: text file with AFNI-usable selector string, which
can be put into either square brackets [] or curly
brackets {}, whichever is appropriate for a given
application.
# ----------------------------------------------------------------------
RUNNING:
fat_proc_select_vols \
-in_dwi DDD \
-in_img IM2D \
{-in_bads TTT} \
-prefix PPP \
{-apply_to_vols} \
{-do_movie AGIF|MPEG} \
{-workdir WWW} \
{-no_cmd_out}
where:
-in_dwi DDD :input DWI set (required).
-in_img IM2D :2d image of DDD, such as made by a fat_proc*
script, or @djunct_*imager directly (required).
-in_bads TTT :(optional) a single column file of integers,
such as made by a previous run of fat_proc_select_vols.
For example, if one has dual phase-encoded
DWI data, then one might make a list of bads
from the AP-acquired set and then add to it any
bad indices from the PA-acquired set.
-prefix PPP :output prefix for files. Required.
-apply_to_vols :switch to apply the created selection of good
volumes to the DWI dset. NB: if you are using
this function to select out bad volumes from
a dual phase encode set, then you *wouldn't* want
to use this option, because you want to apply
the complete removal to *both* volumes. Note also,
that once you apply this selection to the volumes,
you also need to apply it to any bval, bvec, bmatrix,
etc. text files!
-do_movie AGIF | MPEG:
when "-apply_to_vols" is used, static images are
output by default; one can use this option with
either of the given arguments to output a movie of the
newly created dset. Only those arguments can be used
at present.
-workdir WWW :specify a working directory, which can be removed;
(default name = '__WORKING_select_vols').
-no_cmd_out :don't save the command line call of this program
and the location where it was run (otherwise, it is
saved by default in the ODIR/).
# ----------------------------------------------------------------------
EXAMPLE
fat_proc_select_vols \
-in_dwi DWI.nii.gz \
-in_img QC/DWI_sepscl.sag.png \
-prefix DWI_trim
fat_proc_select_vols \
-in_dwi DWI_ap.nii.gz \
-in_img QC/DWI_ap_sepscl.sag.png \
-in_bads DWI_trim_bads.txt \
-prefix DWI_trim_both
# -----------------------------------------------------------------------
