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minctoecat - Online in the Cloud

Run minctoecat in OnWorks free hosting provider over Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

This is the command minctoecat that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

PROGRAM:

NAME


minctecat - convert a minc format file to an Ecat7 format file

SYNOPSIS


minctoecat [<options>] <infile.mnc> <outfile.v>

minctoecat [-help]

DESCRIPTION


minctoecat will convert a 2D image, a 3D volumes or a 4D dynamic volumes written in minc
file format to a 2D, 3D or 4D Ecat7 file. Whereas the Ecat7 format has been designed for
PET volume issued by Ecat scanners (CTI/SIEMENS - Knoxville, TN, USA) it reads any minc
volume type (static PET, dynamic PET, aMRI, fMRI, labels) natively delivered by any
tomograph brand and transform it to a viable Ecat7 file in term of number of dimensions,
dimension size, dimension step, orientation, spatial position, voxel values and voxel
unit. Furthermore, it tries the best as it can to fill optional Ecat7 header fields from
the available minc variables and attributes. By default, it extracts these additional
information from common minc variables, namely: patient_variable, study_variable,
acquisition_variable. In the case of volumes originally delivered by an Ecat PET scanners,
then, other variable are generally available within the minc header:
ecat_acquisition_variable, ecat_main and ecat_sub-header_variable. There, for a such minc
volume, the conversion yields a Ecat7 volume almost identical to the original native
volume in terms of header fields. The user can alter this behaviour using the ignore-list
options (see the option section).

OPTIONS


Note that options can be specified in abbreviated form (as long as they are unique) and
can be given anywhere on the command line.

Command specific options


-ignore_patient_variable: Ignore information from the minc patient variable (MIpatient).

-ignore_study_variable: Ignore information from the minc study variable (MIstudy).

-ignore_acquisition_variable: Ignore information from the minc acquisition variable
(MIacquisition).

-ignore_ecat_accquisition_variable: Ignore information from the minc ecat acquisition
variable (MIecat_acquisition).

-ignore_ecat_main_variable: Ignore information from the minc ecat-mainheader variable
(MIecat-main).

-ignore_ecat_subheader_variable: Ignore information from the minc ecat-subheader variable
(MIecat-subheader).

-no_decay_corr_fctr: do not regenerate the decay correction factors employed as part as
the reconstruction of the original PET volume. The correction factors is a field in the
ecat sub-headers which can be used by processing programs. By default, if the volume is a
PET volume ,those factors are regenerated. This option has no interest in the case of non
PET data.

-label: Treats voxel as integer values instead of floating point values. In this case, the
scale factors and the calibration factors are both set to unity. This option is
particularly useful when the input minc files is a volume of labels.

General options


-help: Print summary of command-line options and abort

-version: Print the program's version and abort

KNOWN BUGS


No bug listed so far :=)

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