fat_proc_convert_dcm_dwis¶
Contents
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The purpose of this function is to help convert one or more sets
of DWIs in DICOM format into 'nicer' volume+grad format. If
multiple directories of DICOMS exist for a given AP or PA set,
then those can be combined into a single volume+grad file with a
single call of this function. Data sets are also converted to have
a single orientation. For data acquired with dual phase encoding
(such as AP/PA, or what is often known as 'blip up'/'blip down'),
separate calls of this function need to be made for each encode
set; however, one can pass origin information to have the same
origin across all volumes during recentering.
This program can be used to: convert dicoms to NIFTI (with bvals
and bvecs); reorient volumetric data; and glue together multiple
sessions/directories of data (may the user choose what is
appropriate to combine!). More functionality could be demanded by
demanding users.
REQUIRES: AFNI (which should now contain dcm2niix_afni, the
version of dcm2niix [by C. Rorden] distributed in AFNI).
Ver. 3.3 (PA Taylor, Feb 20, 2018)
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RUNNING:
fat_proc_convert_dcm_dwis \
-indir DIR \
-prefix PPP \
{-workdir WWW} \
{-orient ORIENT} \
{-origin_xyz X0 Y0 Z0} \
{-flip_x | -flip_y | -flip_z | -no_flip} \
{-reorig_reorient_off} \
{-no_clean} \
{-qc_prefix QCPREF} \
{-no_cmd_out} \
{-no_qc_view} \
{-do_movie AGIF|MPEG}
where:
-indir DIR :directory name(s) of (only) DICOM files of the
DWI data,designated as having 'AP' phase
encoding. DIR can actually contain a wildcard
expression for several directories, if, for
example, multiple DWI sets should be glued
together into one set. NOTE: if specifying more
than one directory, put double quotes around your
entry, like: "file*".
-prefix PPP :set prefix (and path) for output data; will be prefix
for the *.nii.gz, *.bvec and *.bval files. Required.
-orient ORIENT :optional chance to reset orientation of the volume
files (default is currently 'RAI').
-origin_xyz X0 Y0 Z0
:by default, dset will be given an origin value
such that the center of mass of the dset is located
at (x, y, z) = (0, 0, 0), for niceness's sake.
However, an explicit origin can also be given with
this option (NB: this depends on the orientation of
the data, which can various be: explicitly chosen or
set to a default value, or not changed at all).
Three numbers are required to be input (i.e., the
xyz origin values), and this might be useful if, for
example, you've already processed one set of a dual-
phase encoded acquisition, so that you can get the
origin from the first and ensure that the second
has the same values afterwards, making it easier
to overlay the data, should you wish.
-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.)
-flip_x |
-flip_y |
-flip_z |
-no_flip :use any one of these for the ability to flip grads
while processing with 1dDW_Grad_o_Mat++. (Default is
to not flip; it is not necessary to provide that
"-no_flip" option for no flipping to occur.)
-no_clean :switch to not remove working directory of intermediate,
temporary files (default is to delete it).
-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/).
-do_movie AGIF | MPEG
: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.
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OUTPUTS:
For a given phase encoding set, the output files are:
PREFIX.nii.gz # a NIFTI file with N volumes;
PREFIX.rvec # a row-wise (3xN) bvec file of
the (unit-magnitude) gradient orientations;
PREFIX.bval # a row-wise (1xN) bval file of the
gradient magnitudes;
PREFIX_matA.dat # a column-wise (Nx6) AFNI-style matrix file of
the (scaled) b-matrix values;
PREFIX_matT.dat # a column-wise (Nx6) TORTOISE-style matrix file
of the (scaled) b-matrix values;
PREFIX_cvec.dat # a column-wise (Nx3) bvec file of
the (b-magn scaled) gradient orientations;
with the first three meant to mimic the trio of files output by
dcm2niix_afni, and the rest there for convenience.
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EXAMPLE:
fat_proc_convert_dcm_dwis \
-indir "DWI_DICOMS" \
-prefix DWI_UNFILT/dwi
or
fat_proc_convert_dcm_dwis \
-indir dwi_ap \
-prefix DWI_UNFILT/dwi
-do_movie AGIF
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