minctoecat(1)

💖 minctoecat(1) 💖

okay bestie, sit down, we're doing a manual page and honestly? this one ate. it's minctoecat, and it's the glow-up machine that turns your minc files into Ecat7 files. no cap. 🦋

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✨ NAME ✨

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

yes that's literally how the name is spelled in here, i'm not fixing it, i'm just the messenger 💅

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🌸 SYNOPSIS 🌸

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

minctoecat [-help]

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🎀 DESCRIPTION 🎀

so here's the tea, bestie: minctoecat will convert a 2D image, a 3D volume, or a 4D dynamic volume written in minc file format into a 2D, 3D or 4D Ecat7 file. periodt.

now the Ecat7 format was literally designed for PET volumes issued by Ecat scanners (CTI/SIEMENS - Knoxville, TN, USA), but our girl does not gatekeep — she reads any minc volume type (static PET, dynamic PET, aMRI, fMRI, labels) natively delivered by any tomograph brand, and transforms it into a viable Ecat7 file in terms of:

• number of dimensions
• dimension size
• dimension step
• orientation
• spatial position
• voxel values
• voxel unit

and like, that's not even all of it. she also tries the best as she can to fill the optional Ecat7 header fields from whatever minc variables and attributes are available. main character energy, honestly. 👑

by default she extracts this extra info from the common minc variables, namely: patient_variable, study_variable, acquisition_variable.

and okay, special case: if the volumes were originally delivered by an Ecat PET scanner, then other variables are generally available inside the minc header: ecat_acquisition_variable, ecat_main and ecat_sub-header_variable. for a minc volume like that, the conversion yields an Ecat7 volume that's almost identical to the original native volume in terms of header fields. like, obsessed. 😭

and you can always switch up this behaviour with the ignore-list options (see the option section, babe, it's right below).

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💅 OPTIONS 💅

quick vibe check first: options can be specified in abbreviated form (as long as they are unique) and can be given anywhere on the command line. she's flexible like that.

🍓 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

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💀 KNOWN BUGS 💀

No bug listed so far :=)

not a single one. she's perfect. she said so herself. 🙈

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👀 SEE ALSO 👀

ecattominc(1), rawtominc(1), minctoraw(1), dicomtominc(1)

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🌟 AUTHOR 🌟

Anthonin Reilhac (anthonin.reilhac@cermep.fr)

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📜 COPYRIGHTS 📜

Copyrights 2005 by Anthonin Reilhac

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and that's the whole page, bestie — minctoecat(1) in all her glory, copyright 2005, courtesy of Anthonin Reilhac. go convert something iconic. 💖✨🎀