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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 302582882 by agama on Monday 19th of December 2011 01:25:59 AM
Old 12-19-2011
Quote:
Originally Posted by tk0034
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)
Good call -- both creating the test environment and the change to ./...

Quote:

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
Is that file just an oddly named file? The script depends on trNNNN so if the tr is missing odd results will happen.

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

with this??
find ./ -name "*_FA.gz" | while read x
Yep, that will work too. You can run the find command by itself to see what files it finds and thus what files will be candidates for renaming. You can tweek your find to get just the right things and then let its output go into the read. Seems like you are on the right track.
 

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LEARN ABOUT DEBIAN

mcverter

MCVERTER(1)							   User Commands						       MCVERTER(1)

NAME

       mcverter - non-interactive MRI conversion software

SYNOPSIS

       mcverter -o <str> -f <str> [-x] [-d] [-a] [-n] [-b] [-u] [-s <num>] [-m <str>] [-F <str>] [-r] [-v] [-i] [-h] Input directory or file(s)...

DESCRIPTION

       -o, --output=<str>
	      Output directory for converted files

       -f, --format=<str>
	      Output format: fsl, spm, meta, nifti, analyze, or bv

       -x     Save each series to a separate directory

       -d     Save output volumes as 4D files

       -a     Save header only (metaimage only)

       -n, --nii
	      Save files as .nii (nifti/fsl only)

       -b, --v16
	      Save .v16 files (BrainVoyager only)

       -u     Use patient id instead of patient name for output file

       -s, --skip=<num>
	      Skip first n volumes

       -m, --match=<str>
	      Only convert files whose series descriptions include this string

       -F, --fnformat=<str>
	      Use  this  format for name of output file: +/- PatientName, PatientId, SeriesDate, SeriesTime, StudyId, StudyDescription, SeriesNum-
	      ber, SequenceName, ProtocolName, SeriesDescription

       -r, --rescale
	      Apply rescale slope and intercept to data

       -v, --verbose
	      Verbose mode

       -i, --version
	      Version info

       -h, --help
	      Display help

SEE ALSO

       The full documentation for mcverter is maintained as a Texinfo manual.  If the info and mcverter programs are properly  installed  at  your
       site, the command

	      info mcverter

       should give you access to the complete manual.

mcverter 2.0.235						    March 2012							       MCVERTER(1)
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