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Full Discussion: Finding and renaming files with exceptions
Top Forums UNIX for Beginners Questions & Answers Finding and renaming files with exceptions Post 302970467 by azurite on Wednesday 6th of April 2016 09:47:37 PM
Old 04-06-2016
Hello,

Wow! Thank you for taking the time to write great explanations! I have printed it out and will re-read everything to really understand it.

Instead of creating new threads, is it okay if I keep posting new questions in this thread?

If so, I have a question on creating variables. I have tried to research and come up with a solution (to the text quoted below) on my own but I do not know if I am on the right track. If possible could you tell me if I am moving in the right direction?

Quote:
So as far as trying to distinguish between "100_eddy_corrected_brain.nii.gz" and "100_eddy_corrected_brain_mask.nii.gz" if you could define the first as a variable, say $eddy_file or something of the sort, you could pipe it through to a cut command defining a period as your delimiter and take everything in front of it, so something like:
{echo $eddy_file | cut -d. -f1}_mask.nii.gz

But that would depend on using the "set" command to create the variable.
I have come up with the following: though I am not sure what is meant by using the 'set' command.

Code:
#/bin/bash
eddy_file=`cat eddy_corrected_brain.txt`
echo $eddy_file

The eddy_corrected_brain.txt is a text file with pathnames of all the files that match eddy_corrected_brain.nii.gz from the initial find command/results.

Thank you again!
 

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LEARN ABOUT DEBIAN

mnc2nii

mnc2mnc(1)																mnc2mnc(1)

NAME

       mnc2nii - convert a MINC format file to a NIfTI-1 or Analyze format file.

SYNOPSIS

       mnc2nii [<options>] <infile.mnc> <outfile.mnc>

       mnc2nii -help

DESCRIPTION

       The mnc2nii command is used to convert MINC format files to either NIfTI-1 or Analyze format.  The NIfTI-1 format was developed by the mem-
       bers of the Neuroinformatics Technology Initiative's Data Format Working Group (DFWG).  The NIfTI-1 format is based upon the Mayo  Clinic's
       Analyze 7.5 format.

       The  name  of  the program is derived from the common filename suffixes used for NIfTI-1 and MINC files.  NIfTI-1 defines two possible for-
       mats, a "header plus raw image" 2-file format, and a single-file format that includes both header information and the image data.  As  with
       Analyze	7.5, the 2-file format consists of one file with the suffix ".hdr" and another file with the extension ".img".	In NIfTI-1 single-
       file format, the two files may be combined into a single file with a ".nii" filename suffix.

       In addition to the NIfTI-1 formats, mnc2nii can convert MINC files to the Analyze 7.5 format.

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.

Output file format
       -dual  Save file in NIfTI-1 two-file format (.hdr and .img)

       -ASCII Save file in non-standard NIfTI-1 ASCII file format

       -nii   Save file in NIfTI-1 single-file format (.nii)

       -analyze
	      Save file in Analyze 7.5 compatible format

Output voxel format
       -float Save voxels in 32-bit floating point format

       -double
	      Save voxels in 64-bit floating point format

       -byte  Save voxels in 8-bit integer format

       -short Save voxels in 16-bit integer format

       -int   Save voxels in 32-bit integer format

       -signed
	      Save voxels in signed (2's complement) integer format

       -unsigned
	      Save voxels in unsigned integer format

Other options
       -noscanrange
	      Don't scan data to determine valid range.

       -quiet Quiet operation - do not print progress or debugging information.

Generic options for all commands
       -help  Print summary of command-line options and abort

       -version
	      Print the program and library versions and abort

KNOWN BUGS

       Current handling of NIfTI-1 qform and sform coordinate transforms should probably be revised as the NIfTI group clarifies the correct usage
       of these fields.

SEE ALSO

       nii2mnc

AUTHOR

       Robert Vincent (bert@bic.mni.mcgill.ca) with assistance from the NIfTI-1 library authored by Robert Cox et al.

COPYRIGHTS

       Copyrights 2005 by Robert Vincent for the Montreal Neurological Institute.

$Revision: 1.3 $						    Apr 22 2005 							mnc2mnc(1)
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