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.TH "DCM2NIIX" "1" "Jun 03, 2017" "1.0" "dcm2niix"
.SH NAME
dcm2niix \- DICOM to NifTI converter
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.SH SYNOPSIS
.sp
\fBdcm2niix\fP [\fIoptions\fP] <\fIsourcedir\fP>
.SH DESCRIPTION
.sp
Most medical imaging devices save images in some variation of the popular DICOM
format. However, most scientific tools expect medical images to be stored in
the comparatively simpler NIfTI format. \fBdcm2niix\fP is designed to perform
such conversion from DICOM to NIfTI with a simple command\-line interface.
.sp
Please be advised that \fBdcm2niix\fP has been developed for research purposes
only and should not be considered a clinical tool.
.SH OPTIONS
.INDENT 0.0
.TP
.BI \-b \ <y/n>
Save additional BIDS metadata to a side\-car .json file.
.TP
.BI \-f \ <format>
Format string for the output filename(s). The following
specifiers are supported:
.INDENT 7.0
.IP \(bu 2
%a, antenna (coil) number
.IP \(bu 2
%c, comments
.IP \(bu 2
%d, description
.IP \(bu 2
%e, echo number
.IP \(bu 2
%f, folder name
.IP \(bu 2
%i, patient ID
.IP \(bu 2
%m, manufacturer
.IP \(bu 2
%n, patient name
.IP \(bu 2
%p, protocol
.IP \(bu 2
%s, series number
.IP \(bu 2
%t, time
.IP \(bu 2
%u, acquisition number
.IP \(bu 2
%z, sequence name.
.UNINDENT
.sp
The default format string is "%p_%e_%4s".
.TP
.BI \-m \ <y/n>
Merge slices from the same series regardless of study time,
echo, coil, orientation, etc...
.TP
.BI \-o \ <path>
Output directory where the converted files should be saved. If
unspecified, the files are saved within the specified source
directory.
.TP
.BI \-s \ <y/n>
Convert a single file only.
.TP
.BI \-t \ <y/n>
Save patient details.
.TP
.BI \-v \ <h/y/n>
Enable verbose output. "n" for succinct, "y" for verbose, "h" for
high verbosity
.TP
.BI \-x \ <y/n>
Crop images.
.TP
.BI \-z \ <y/i/n>
Desired compression method. The "y"es option uses the external
program pigz if available. The "i" option compresses the image
using the slower built\-in compression routines.
.UNINDENT
.SH LICENSING
.sp
Copying and distribution of this file, with or without modification, are
permitted in any medium without royalty provided the copyright notice and this
notice are preserved. This file is offered as\-is, without any warranty.
.SH AUTHOR
This manual was developed and is maintained by Ghislain Antony Vaillant <ghisvail@gmail.com>
.SH COPYRIGHT
2017 The dcm2niix contributors
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