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Full Discussion: rename files based on their respective directory name
Top Forums UNIX for Dummies Questions & Answers rename files based on their respective directory name Post 302582879 by tk0034 on Monday 19th of December 2011 01:13:28 AM
Old 12-19-2011
this is so great. thank you!

So I copied one entire directory (tr9915_gray) to a separate "test folder" (/Data/DTI_test) to try it out. I ran the script from this test folder and so I thought I should replace the first line:
find /Data -name "*.gz" | while read x
with this:
find ./ -name "*.gz" | while read x
(not sure if I should have done that)

It seemed to work, except the thing is, there are a lot of files that end in .gz in various subdirectories.... and it renamed all the files ending in .gz in the subdirectories of /tr9915_gray and skipped the ones in /tr9915_gray/tr9915_DTI. Here is an example of the last three lines from the output.

mv ./tr9915_gray/MSIT_PPI_MFG_ROI.feat/reg/highres.nii.gz ./tr9915_gray/MSIT_PPI_MFG_ROI.feat/reg/9915_highres.nii.gz
mv ./tr9915_gray/MSIT_PPI_MFG_ROI.feat/reg/highres2standard.nii.gz ./tr9915_gray/MSIT_PPI_MFG_ROI.feat/reg/9915_highres2standard.nii.gz
mv ./8531_dti_FA.nii.gz ././8531_8531_dti_FA.nii.gz

Not really sure what happened with the last line at all!
Since I just want to rename the file called dti_FA.nii.gz which resides in /tr9915_gray/tr9915_DTI

...could I replace the first line you made:
find ./ -name "*.gz" | while read x

with this??
find ./ -name "*_FA.gz" | while read x

thank you again so much!!
 

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LEARN ABOUT DEBIAN

vbim

vbim(1) 							 The VoxBo Manual							   vbim(1)

NAME

       vbim - manipulate 3D and 4D volumes

SYNOPSIS

       vbim <flag> ...

DESCRIPTION

       vbim is part of the VoxBo suite of tools for brain image analysis.

       vbim is a multi-purpose program that applies various simple manipulations to 3D and 4D images.

OPTIONS

       vbim performs a set of operations, specified by option flags, in sequence.  To get a complete list of available flags, run the program with
       no arguments.

EXAMPLES

       To get very basic info about a file:

	      vbim foo.nii -info

       To get more detailed information about the data within a mask:

	      vbim foo.nii -regioninfo mask.nii

       To apply a mask to a 3D image and write out the result:

	      vbim image.nii -mask mask.nii -write maskedimage.nii

       To mask a 4D image:

	      vbim image.nii -mask mask.nii -write4D maskedimage.nii

       To average a bunch of 3D volumes:

	      vbim *.nii.gz -average -write mean.nii.gz

       To create a lesion count map from a set of lesion masks:

	      vbim *.nii -count -write count.nii.gz

       To create a 4D volume (20x20x20 voxels, 32-bit int, 10 time points) of random data with a mean of 100 and sd of 10:

	      vbim -newvol 20 20 20 10 int32 -addnoise 100 10 -write3d myvol.nii

NOTES

AVAILABILITY

       Pre-built VoxBo binaries are available for Linux, OSX, and Cygwin, and via the NeuroDebian project (neuro.debian.net)  for  Debian  deriva-
       tives.

CAVEATS

       VoxBo is provided with no warranty whatsoever.

AUTHOR

       For an historical roster of the VoxBo development team, visit www.voxbo.org.

SEE ALSO

       For  detailed  help  on	any VoxBo command-line program, run it with no arguments.  For graphical programs, use the -h flag.  For more help
       with VoxBo, for information about the mailing list, or to report bugs, visit the web site at www.voxbo.org.

       For information about file format support in VoxBo, see voxbo-fileformats(7).  For general information about VoxBo, see voxbo(7).

VoxBo							      January, 2011 (v1.8.5)							   vbim(1)
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