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'''Index'''
<<TableOfContents>>


= Name =
mri_convert_mdh - Probes or converts Siemens propietary format (MDH) to MGH format

= Synopsis =
|| mri_convert_mdh --srcdir || Probes source directory, prints out MDH file parameters to stdout file||
|| mri_convert_mdh --srcdir --outdir || Converts MDH file to MGH format ||

= Arguments =
== Positional Arguments ==
|| dim nframes nslices nechoes nlines nperline npcns ||
|| fasterdim dimname ||
|| TR TR ||
|| TE TE1 TE2 ||

== Required Arguments ==
|| -srcdir dir || directory with meas.out and ascii file || contains k-space data in Siemens format ||

== Description ==
Directory with the meas.out file and the ascii file. The meas.out file
contains the measured k-space data in Siemens MDH format (which includes
miniheaders). The meas.out file must be accompanied by an ascii file
called either MrProt.asc or mrprot.asc (NUMARIS 4 VA15) or meas.asc
(NUMARIS 4 VA21). The version is determined by the name of this file.



== Optional Arguments ==
|| --outdir dir || directory where output stored || if this doesn't exist, it will be created ||
|| --rev || reverse readouts for even lines ||DOES NOT WORK YET ||
|| --dump || print header info || provides header info for each line, but not for the ADC data itself. Only the source directory is needed ||
|| --adcstats || prints min, max, and avg over all ADCs || good for finding spikes. Only the source directory is needed ||
|| --help || a short story about a Spanish boy named Manual ||


= Outputs =
|| outdir dir || Directory where output will be stored-will be created if it does not already exist ||
|| stdout || MDH file parameters(Probe results) ||
|| pcnr.mgh || Phase correction navigators (real)||
|| pcni.mgh || Phase correction navigators (imaginary)||
|| echoNr || Echo (real) where N is the echo number (starting with 0)||
|| echoNi.mgh || Echo (imaginary) where N is the echo number (starting with 0)||

= Description =

If an output directory does not exist, it will be created (only for one level).

If an output directory is not specified, then the MDH file is probed,
and the various parameters are printed to stdout.

When an output is specified, the output will have two parts: phase
correction navigators and echos.  The phase correction navigators will
be stored in pcnr.mgh (real) and pcni.mgh (imaginary).  The echos will
be stored in echoNr.mgh (real) and echoNi.mgh (imaginary), where N is
the echo number (starting with 0).

= Examples =
== Example 1 ==




== Example 2 ==




= Bugs =
Does not handle version V21 yet.<<BR>>
Does not handle 3D sequences yet.<<BR>>
Does not handle FLASH  sequences yet.<<BR>>
Does not handle multiple channels yet.<<BR>>

--rev argument should reverse lines for even number echos, but does not do this yet.

= See Also =


= Links =
FreeSurfer, FsFast

= Methods Description =
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}}}

= References =


= Reporting Bugs =
Report bugs to <analysis-bugs@nmr.mgh.harvard.edu>

= Author/s =