ecattominc(1) [debian man page]
ecattominc(1) ecattominc(1) NAME
ecattominc - convert an ecat format file (version 6.x or 7.x) to a minc format file SYNOPSIS
ecattominc [<options>] <infile> <outfile.mnc> ecattominc [-help] DESCRIPTION
ecattominc will convert an ecat data file (version 6.x or 7.x) to a minc file format Unless the -small_header option is specified, ecattom- inc will conserve the maximum informations from the ecat header and subheader fields which will be respectively stored as attributes of the ecat-main and ecat-subhdr minc variables. By default the whole 3D or 4D volume is converted, however, ecattominc allows for the selection of slice and frame ranges to be copied. The voxel values of the generated minc file are decay corrected, unless the nodecay_correct flag is specified. Finally, blood data file can be inserted within the minc file with the -bloodfile option. 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. General options -byte: Write out data as bytes (default). -short: Write out data as short integers. -clobber: Overwrite existing file. -noclobber: Don't overwrite existing file (default). -verbose: List files as they are converted (default) -quiet: Do not list files as they are converted. Command specific options -decay_correct: Do decay correction on images (default). -nodecay_correct: Don't do decay correction. -slices:Range of slices to copy (counting from 0). Default value: -2147483648 -2147483648 -frames: Range of frames to copy (counting from 0). Default value: -2147483648 -2147483648 -frame: Single frame to copy (counting from 0). Default value: -2147483648 -small_header: Copy only basic header information. -all_header: Copy all header information (default). -bloodfile: Insert blood data from this file. Generic options for all commands -help: Print summary of command-line options and abort KNOWN BUGS
No bug listed so far :=) SEE ALSO
minctoecat(1), rawtominc(1), minctoraw(1), dicomtominc(1) AUTHOR
Peter Neelin and Anthonin Reilhac (anthonin.reilhac@cermep.fr) COPYRIGHTS
Copyrights 2005 by Peter Neelin ecattominc(1)
Check Out this Related Man Page
MINCAVERAGE(1) MINC User's Guide MINCAVERAGE(1) NAME
mincaverage - average minc files SYNOPSIS
mincaverage [<options>] <in1>.mnc [<in2>.mnc...] <out>.mnc DESCRIPTION
Mincaverage averages minc files together. A range of optional behaviour is permitted as well: pre-normalizing volumes, creating a standard deviation volume, averaging over a specified dimension of the input files. 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. General options -2 Create a MINC 2.0 format output file. -clobber Overwrite an existing file. -noclobber Don't overwrite an existing file (default). -verbose Print out progress information for each chunk of data copied (default). -quiet Do not print out progress information. -debug Print extra information (e.g. normalization factors). -filelist filename Specify a file containing a list of input file names. If "-" is given, then file names are read from stdin. If this option is given, then there should be no input file names specified on the command line. Empty lines in the input file are ignored. -max_buffer_size_in_kb buffer-size Specify the maximum size of the internal buffers (in kbytes). Default is 4096 kbytes. Output type options These options control the storage precision and size of individual voxel values in the output file. -filetype Don't do any type conversion (default). -byte Write out 8-bit integer values. -short Write out 16-bit integer values. -int Write out 32-bit integer values. -long Superseded by -int. -float Write out single-precision floating point values. -double Write out double-precision floating point values. -signed Write out values as signed integers (default for short and long). Ignored for floating point types. -unsigned Write out values as unsigned integers (default for byte). Ignored for floating point types. -range min max specifies the valid range of output voxel values in their integer representation. Default is the full range for the type and sign. This option is ignored for floating point values. For it to have any effect, you must specify a type. Averaging options -normalize Normalize volumes to their global average before averaging them (based on the mean of voxels with value greater than 2 percent of full range above the minimum). -nonormalize Do not normalize volumes (default). -sdfile sdfile.mnc Specify the name of an output standard deviation file, to be calculated in addition the mean that is normally calculated. -copy_header Copy all of the additional header information from the first input file (default for one input file). -nocopy_header Do not copy additional header information (default for many input files). -avgdim dimname Specify the name of a dimension over which we should be averaging (or calculating standard deviation). If normalization is done, it still only applies to separate files only - no normalization is done within a file. -binarize Binarize the input volumes before calculating the average. The binarization is done by specifying a range of values that contribute 1 to the average. Normalization of the input is not permitted when performing binarization. -binrange min max Specify the range of values for binarization. -binvalue value Specify a single legal value (integer) for binarization. The range is set to be +/- 0.5 around this value to achieve an effective rounding of input values. -weights <w1,w2,...> Specify a series of weights for averaging. The number of weighting values must match the number of input files and the values must be provided as a single argument with commas or spaces as separators. The sum of the weights must be non-zero. If weights are used with an averaging dimension, then only one input file can be specified. -width_weighted This option can only be used when averaging across a dimension (-avgdim option). It specifies that weighting should be done using the width variable that corresponds to the averaging dimension. For example, using -width_weighted with -avgdim time will use the time-width variable to weight the values. Generic options for all commands: -help Print summary of command-line options and exit. -version Print the program's version number and exit. AUTHOR
Peter Neelin COPYRIGHTS
Copyright (C) 1995 by Peter Neelin $Date: 2004-05-20 21:52:07 $ MINCAVERAGE(1)