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= Name =
mri_parse_sdcmdir - parses the DICOM files in a given directory

= Synopsis =
mri_parse_sdcmdir --d sdicomdir [<options>]

= Arguments =
== Positional Arguments ==
none

== Required Flagged Arguments ==
|| --d sdicomdir || path to siemens dicom directory || this is the name of the directory where the dicom files are located (required) ||

== Optional Flagged Arguments ==
|| --o outfile || write results to outfile (default is stdout) || this is the name of the file to which the result will be printed.  if unspecified, the results will be printed to stdout ||
|| --sortbyrun || assign run numbers || ||
|| --summarize || only print out info for run leaders || forces print out of information for the first file in the run ||
|| -- help || how to use this program || ||
 
= Outputs =
|| stdout or outfile || spreadsheet containing information about the DICOM files in a given directory ||

= Description =
mri_parse_sdcmdir parses the Siemens DICOM files in a given directory, and prints out information about each file.  the output is printed to stdout unless a file name is passed with the --o flag

the most useful information is that which cannot be easily obtained by probing a dicom file.  this includes:  the run number, number of frames in the run, number of slices in the run, and, for mosaics, the number of rows and cols in the volume

there are 14 columns in the output:
  1. File Number
  2. File Name 
  3. Series Number
  4. Series Error Flag (1 for error)
  5. Image Number
  6. Mosaic Flag   (1 for mosaics)
  7. Number of Rows    in the Volume
  8. Number of Columns in the Volume
  9. Number of Slices  in the Volume for the Series
 10. Number of Frames in the Series
 11. Repetition Time (sec)
 12. Echo Time (ms)
 13. Protocol Name - white space stripped 

= Examples =
== Example 1 ==
??

== Example 2 ==
??

= Bugs =
None

= See Also =
[[othercommand1]], [[othercommand2]]

= Links =
FreeSurfer, FsFast

= Methods Description =
{{{
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}}}

= References =
[[References/Lastname###]]

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

= Author/s =
BruceFischl