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# 1  
Old 07-06-2016
Add part of pathname/subfolder name to beginning of filename
Hello everyone,
I need some help renaming files. I have a directory with a bunch of subfolders in it like so with DWI being the working directory and the 3 levels after it being subdirectories
Code:
home/user/Documents/DWI/111180-100/3t_2016-01-07_21-42/003_DTI_siemens_TClessdistort/dtifit_FA.nii.gz
home/user/Documents/DWI/111445-100/3t_2016-01-07_21-42/003_DTI_siemens_TClessdistort/dtifit_FA.nii.gz
etc

Those subfolders all have a couple of files that begin with 'dti' and end in 'nii.gz'
Code:
(ex: dti_FA.nii.gz, dti_V1.nii.gz etc)

I need a script that will loop over all the subfolders and rename the file so that it adds the bolded part of the pathname to the beginning of the file. Example:

Code:
home/user/Documents/DWI/111180-100/3t_2016-01-07_21-42/003_DTI_siemens_TClessdistort/dtifit_FA.nii.gz
home/user/Documents/DWI/111445-100/3t_2016-01-07_21-42/003_DTI_siemens_TClessdistort/dtifit_FA.nii.gz

to rename the file in each subfolder from
Code:
 'dti_FA/V1etc.nii.gz' to 'specifiedstringfrompath_dti_*.nii.gz' or '111180-100_dti_FA/V1etc.nii.gz'

I know I need to use the for loop and perhaps globbing but I don't know how to go about adding that string from the subdirectory to the file?
# 2  
Old 07-06-2016
We can't really begin to help until we know your:-

1) Operating System.
2) Which shell is allowed.
3) What machine(s) it is to be run on.
Etc, etc...

We can assume 'bash' but it could just as easily be 'csh' as both are so radically different as to require almost totally different approaches.
# 3  
Old 07-06-2016
If I recall correctly, Ubuntu 12.4 and bash were mentioned in an earlier thread... so, try
Code:
find home/user/Documents/DWI -type f -name "dti*nii.gz" | while read FN; do TMP=${FN#*/*/*/*/}; TMP=${TMP%%/*}; echo mv $FN ${FN/dti/${TMP}_dti}; done 
mv home/user/Documents/DWI/111180-100/3t_2016-01-07_21-42/003_DTI_siemens_TClessdistort/dtifit_FA.nii.gz home/user/Documents/DWI/111180-100/3t_2016-01-07_21-42/003_DTI_siemens_TClessdistort/111180-100_dtifit_FA.nii.gz
mv home/user/Documents/DWI/111445-100/3t_2016-01-07_21-42/003_DTI_siemens_TClessdistort/dtifit_FA.nii.gz home/user/Documents/DWI/111445-100/3t_2016-01-07_21-42/003_DTI_siemens_TClessdistort/111445-100_dtifit_FA.nii.gz

The echo is in there to stay on the safe side; remove it when you're happy with the "proposed" result.
Am I right in guessing the /V1etc in your sample results is an undesired artefact?
# 4  
Old 07-06-2016
Quote:
Originally Posted by RudiC
If I recall correctly, Ubuntu 12.4 and bash were mentioned in an earlier thread... so, try
Code:
find home/user/Documents/DWI -type f -name "dti*nii.gz" | while read FN; do TMP=${FN#*/*/*/*/}; TMP=${TMP%%/*}; echo mv $FN ${FN/dti/${TMP}_dti}; done 
mv home/user/Documents/DWI/111180-100/3t_2016-01-07_21-42/003_DTI_siemens_TClessdistort/dtifit_FA.nii.gz home/user/Documents/DWI/111180-100/3t_2016-01-07_21-42/003_DTI_siemens_TClessdistort/111180-100_dtifit_FA.nii.gz
mv home/user/Documents/DWI/111445-100/3t_2016-01-07_21-42/003_DTI_siemens_TClessdistort/dtifit_FA.nii.gz home/user/Documents/DWI/111445-100/3t_2016-01-07_21-42/003_DTI_siemens_TClessdistort/111445-100_dtifit_FA.nii.gz

The echo is in there to stay on the safe side; remove it when you're happy with the "proposed" result.
Am I right in guessing the /V1etc in your sample results is an undesired artefact?
Yes, I am working with bash, ubuntu 12.4.

Will this code rename the files in a batch. I need to rename all the files, inside all subfolders, that begin with "dti". Is there a way I can do the same with a for loop or shopt glob?

Here is a sample of the directory structure. There are many more subfolders but I've only shown 3 for the purposes of keeping it short.

Code:
├── 111180-100
│** └── 3t_2016-01-07_21-42
│**     └── 003_DTI_siemens_TClessdistort
│**         ├── 0001.dcm
│**         ├── 111180-100_eddy_corrected_brain_mask.nii.gz
│**         ├── 111180-100_eddy_corrected_brain.nii.gz
│**         ├── 111180-100_eddy_corrected.ecclog
│**         ├── 111180-100_eddy_corrected.nii.gz
│**         ├── 20160107_214213DTIsiemensTClessdistorts003a001.bval
│**         ├── 20160107_214213DTIsiemensTClessdistorts003a001.bvec
│**         ├── 20160107_214213DTIsiemensTClessdistorts003a001.nii.gz
│**         ├── dti_FA.nii.gz
│**         ├── dti_L1.nii.gz
│**         ├── dti_L2.nii.gz
│**         ├── dti_L3.nii.gz
│**         ├── dti_MD.nii.gz
│**         ├── dti_MO.nii.gz
│**         ├── dti_S0.nii.gz
│**         ├── dti_V1.nii.gz
│**         ├── dti_V2.nii.gz
│**         └── dti_V3.nii.gz
├── 111405-100
│** └── 3t_2015-12-08_21-54
│**     └── 003_DTI_siemens_TClessdistort
│**         ├── 0001.dcm
│**         ├── 111405-100_eddy_corrected_brain_mask.nii.gz
│**         ├── 111405-100_eddy_corrected_brain.nii.gz
│**         ├── 111405-100_eddy_corrected.ecclog
│**         ├── 111405-100_eddy_corrected.nii.gz
│**         ├── 20151208_215447DTIsiemensTClessdistorts003a001.bval
│**         ├── 20151208_215447DTIsiemensTClessdistorts003a001.bvec
│**         ├── 20151208_215447DTIsiemensTClessdistorts003a001.nii.gz
│**         ├── dti_FA.nii.gz
│**         ├── dti_L1.nii.gz
│**         ├── dti_L2.nii.gz
│**         ├── dti_L3.nii.gz
│**         ├── dti_MD.nii.gz
│**         ├── dti_MO.nii.gz
│**         ├── dti_S0.nii.gz
│**         ├── dti_V1.nii.gz
│**         ├── dti_V2.nii.gz
│**         └── dti_V3.nii.gz
├── 111440-100
│** └── 3t_2016-01-27_20-58
│**     └── 003_DTI_siemens_TClessdistort
│**         ├── 0001.dcm
│**         ├── 111440-100_eddy_corrected_brain_mask.nii.gz
│**         ├── 111440-100_eddy_corrected_brain.nii.gz
│**         ├── 111440-100_eddy_corrected.ecclog
│**         ├── 111440-100_eddy_corrected.nii.gz
│**         ├── 20160127_205836DTIsiemensTClessdistorts003a001.bval
│**         ├── 20160127_205836DTIsiemensTClessdistorts003a001.bvec
│**         ├── 20160127_205836DTIsiemensTClessdistorts003a001.nii.gz
│**         ├── dti_FA.nii.gz
│**         ├── dti_L1.nii.gz
│**         ├── dti_L2.nii.gz
│**         ├── dti_L3.nii.gz
│**         ├── dti_MD.nii.gz
│**         ├── dti_MO.nii.gz
│**         ├── dti_S0.nii.gz
│**         ├── dti_V1.nii.gz
│**         ├── dti_V2.nii.gz
│**         └── dti_V3.nii.gz
└── example

# 5  
Old 07-06-2016
Did you try it? It will echo only, i.e. just propose what it would do...
# 6  
Old 07-06-2016
Quote:
Originally Posted by RudiC
Did you try it? It will echo only, i.e. just propose what it would do...
Okay, it worked. I just had to add a few more asterisks. Could you explain what the code/syntax does? Where do I learn all these?
# 7  
Old 07-07-2016
Why and where did you add asterisks? Above should find exactly what you asked for in post#1. To learn all this, you need to code, again and again, read documentation (like man find), accept and interpret error messages, optimize your code. We're here to help you doing that.
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