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The purpose of this function is to help convert an anatomical data
set from DICOM files into a volume. Ummm, yep, that's about it.
(But it will be done in a way to fit in line with other
processing, particularly with DTI analysis, so it might not be
*totally* useless; more options while converting might be added
over time, as well.)
REQUIRES: AFNI (which should now contain dcm2niix_afni, the
version of dcm2niix [by C. Rorden] distributed in AFNI).
Ver. 3.52 (PA Taylor, Sep 27, 2021)
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RUNNING:
fat_proc_convert_dcm_anat \
{-indir DIR_IN | -innii NII_IN} \
-prefix PPP \
{-workdir WWW} \
{-orient ORIENT} \
{-no_clean} \
{-reorig_reorient_off} \
{-qc_prefix QCPREF} \
{-no_cmd_out} \
{-no_qc_view}
where:
-indir DIR_IN :input as dicom directory; DIR_IN should contain
only DICOM files; all will be selected.
-innii NII_IN :input as NIFTI file (zipped or unzipped fine).
Alternative to '-indir ..'. The point of this option
is to have all other "niceifying" steps applied
to an already-converted volume.
-prefix PPP :set prefix (and path) for output data; required.
-workdir WWW :specify a working directory, which can be removed;
(default name = '__WORKING_convert_dcm_anat').
-orient ORIENT :optional chance to reset orientation of the volume
files (default is currently 'RAI').
-reorig_reorient_off
:switch to turn of the nicety of putting (0, 0, 0)
at brain's center of mass (-> 'reorigin' calc) and to
not reorient data (-> 'reorient' calc). Could lead
to weirdness later on down the road, depending on the
data and headers (ergo, not recommended.)
-qc_prefix QCPREF :can set the prefix of the QC image files separately
(default is '').
-no_qc_view :can turn off generating QC image files (why?)
-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/).
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OUTPUTS: a single anatomical volume in the DIR_OUT.
In some cases of anatomical volume acquisition, the DICOMS
get converted to more than one format of volumetric output
(one total acquired volume, one centered around the head,
etc.); these usually have different formats of file name,
starting with '2*', 'co*' and 'o*'. Basically, the '2*' is
chosen for outputting, and the others are stored in a
subdirectory called DIR_OUT/WWW/.
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EXAMPLES:
fat_proc_convert_dcm_anat \
-indir "ANAT_DICOMS" \
-prefix outdir/anat \
-orient RAI
fat_proc_convert_dcm_anat \
-innii t1w.nii.gz \
-prefix outdir/anat \
-orient RAI
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