# HG changeset patch
# User bert <bert>
# Date 1121363965 0
# Node ID e029c25a01f49a6a8078b57f6c45c34501b0a30b
# Parent  9e9cc64678e497a81db925bba003549c94cd9f89
latest updates to man page

diff --git a/conversion/dcm2mnc/dcm2mnc.man1 b/conversion/dcm2mnc/dcm2mnc.man1
--- a/conversion/dcm2mnc/dcm2mnc.man1
+++ b/conversion/dcm2mnc/dcm2mnc.man1
@@ -1,4 +1,4 @@
-.TH dcm2mnc 1 "May 03 2005" "$Revision: 1.2 $" ""
+.TH dcm2mnc 1 "May 03 2005" "$Revision: 1.3 $" ""
 .SH NAME
 
 .B dcm2mnc
@@ -80,6 +80,17 @@
 stored in a single MINC file with a "time" dimension.  If this option is
 specified, each time slice will be saved in a separate file.
 
+.TP
+.BI -fname " <format-spec>"
+Set the format of the output file name. See FILENAMES section for
+details on this option.
+
+.TP
+.BI -dname " <format-spec>"
+Set the format of the output subdirectory name. See FILENAMES section for
+details on this option. Set this to the empty string to avoid creating a
+subdirectory.
+
 .SH "Siemens mosaic specific options"
 These two options control the manner in which Siemens mosaic data is 
 converted.  Siemens scanners commonly represent fMRI data as a "mosaic"
@@ -153,9 +164,74 @@
 .BI -version
 Print the program and library versions and abort
 
+.SH FILENAMES
+
+To avoid naming collisions when converting a large set of input DICOM
+files to a smaller set of MINC output files, 
+.B dcm2mnc
+automatically generates the names of output files according to various
+parameters of the DICOM file information.  The normal behavior is to
+place all of the output files in a subdirectory of the given output
+directory which has its name derived from the patient's name and the
+study date and time as follows:
+
+patientname\_yyyymmdd\_hhmmss/
+
+The individual files are named according to the patient name, study date
+and time, series identifer, and modality information as follows:
+
+patientname\_yyyymmdd\_hhmmss\_series\_scan\_modality.mnc
+
+The optional scan information includes the echo number ('e<n>'), slice
+number ('sl<n>'), time series position ('d<n>'), phase number ('p<n>'),
+or chemical shift ('cs<n>').
+
+The optional modality information consists of either the string "_pet"
+or "_mri".  No suffix is added for unrecognized modalities.
+
+The 
+.B -fname
+and 
+.B -dname
+commands allow the user to override the standard file naming behavior by
+specifying alternative output directory and file formats.  The arguments
+to these options are template strings that will be expanded to include
+information from the DICOM sequences in specified
+locations. Replacements are specified by a '%' character followed by a
+single alphabetic character, as follows:
+
+    %N - Name of patient
+    %D - Date of scan
+    %T - Time of scan
+    %S - Study ID (typically 'yyyymmdd.hhmmss')
+    %A - Acquisition or series ID
+    %s - Optional slice label
+    %e - Optional echo number
+    %t - Optional dynamic scan number
+    %p - Optional phase number
+    %c - Optional chemical shift number
+    %m - Optional modality
+
+The default file name convention is therefore given by the format
+string:
+
+%N_%D_%T_%A%s%e%t%p%c%m
+
+and the default directory name is given by the format string:
+
+%N_%D_%T
+
+If you wish to avoid creating a subdirectory, you may do so by giving a
+zero-length string as the argument to the
+.B -dname
+option:
+
+dcm2mnc -dname \'\' filenames...
+
+
 .SH AUTHORS
 Peter Neelin
-Rich Hoge
+Richard D. Hoge
 
 Please direct all complaints and inquiries to Robert Vincent 
 (bert@bic.mni.mcgill.ca)
@@ -163,7 +239,7 @@
 .SH BUGS
 
 Probably many. For best results, output files should be checked by a
-compenent human to verify that the conversion was performed properly.
+competent human to verify that the conversion was performed properly.
 DICOM is a very complex format, and it is difficult to anticipate all of
 the possible combinations of fields and values that may be encountered.
 If you have a problem, please contact the maintainer.  It will be