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.
10 More Discussions You Might Find Interesting
1. Shell Programming and Scripting
i have hundreds of directories that have to be renamed. the directory structure is fairly uniform which makes the scripting a little simpler.
suppose i have many directories like this */*/*/*abc* (in other words i have similar directory names 3 dirs deep that all contain the pattern abc in... (8 Replies)
Discussion started by: quantumechanix
8 Replies
2. Shell Programming and Scripting
Hi,
I'm not very experienced in shell scripting and that's probably why I came across the following problem:
I do have several hundred pairs of text files (PF00x.spl and PF00x.shd) where the first file (PF00x.spl) needs to be renamed according a string that is included in the second file... (12 Replies)
Discussion started by: inCH
12 Replies
3. Shell Programming and Scripting
Hi,
I have around 100 xml file in a directory. I need to rename the files from .xml to .xml1. So i tried using the following command:
mv *.xml *.xml1
but i am getting the following error
mv: when moving multiple files, last argument must be a directory
Try `mv --help' for more... (8 Replies)
Discussion started by: ananthi_ku
8 Replies
4. UNIX for Dummies Questions & Answers
Dear friends,
I have created a script to rename all files in a directory by appending the file name with username (who created the file), the date it was created. For example, "apple.doc" should be renamed to "johnFeb23apple.doc" where "john" is the owner and "Feb23" is file created date. It... (4 Replies)
Discussion started by: djsnifer
4 Replies
5. Shell Programming and Scripting
How can i rename list of files in a directory? (4 Replies)
Discussion started by: knip
4 Replies
6. UNIX for Dummies Questions & Answers
I have a directory e2e_ms_xfer/cent01
this contains the multiple files some of which will be named below with unique date time stamps
e2e_ms_edd_nom_CCYYMMDD_HHMM.csv
What I want to do is in a loop
1) Get the oldest file
2) Rename
3) Move it up one level from e2e_ms_xfer/cent01 to... (1 Reply)
Discussion started by: andymay
1 Replies
7. Shell Programming and Scripting
Hi All,
I am creating a script which will connect to remote server with ssh and perfom below.
- Search in a directory
- Search for a pattern
- Check the size if greater than the size_limit rename the file.
Below is the code i have written.
ssh user@host <<EOF
find /tmp... (5 Replies)
Discussion started by: Girish19
5 Replies
8. UNIX for Dummies Questions & Answers
Hi,
I have a directory with a lot of files like this:
a.bam
b.bam
c.bam
I like to rename these files based on a list where the name of the files in the first column will be replasced by the names in the second column. Here is my list which is a tab-delimited text file:
a x
b y
c ... (4 Replies)
Discussion started by: a_bahreini
4 Replies
9. Shell Programming and Scripting
Hello, I have a text file "file.list" with the contents below.
file1
filename1
file2
filename2
file3
filename3
file1, file2 and file3 are files existing in the same directory as the text file file.list.
I want to rename file1 to filename1, file2 to filename2, as show in the text... (1 Reply)
Discussion started by: james2009
1 Replies
10. UNIX for Beginners Questions & Answers
Hello!
New here although not completely new to Unix.
I wonder how I could rename files based on the data found in a simple textfile.
It goes like this:
I have 4 files
1 ldfgkkfjslkdfjsldkfjsf.wav
2 nndsdflksdjf.wav
3 sdflksjdf jjsdflsdfl.wav
4 dkadsdddd.wav
Textfile.txt looks like... (14 Replies)
Discussion started by: Oortone
14 Replies
LEARN ABOUT DEBIAN
dcm2nii
DCM2NII(1) User Commands DCM2NII(1)
NAME
dcm2nii - convert DICOM or PAR/REC image into the NIfTI format
SYNOPSIS
dcm2nii <options> <sourcenames>
OPTIONS
-a Anonymize [remove identifying information]: Y,N = Y
-b load settings from specified inifile, e.g. '-b /etc/mricron.ini'
-c Collapse input folders: Y,N = N
-d Date in filename [filename.dcm -> 20061230122032.nii]: Y,N = Y
-e events (series/acq) in filename [filename.dcm -> s002a003.nii]: Y,N = Y
-f Source filename [e.g. filename.par -> filename.nii]: Y,N = Y
-g gzip output, filename.nii.gz [ignored if '-n n']: Y,N = Y
-i ID in filename [filename.dcm -> johndoe.nii]: Y,N = Y
-n output .nii file [if no, create .hdr/.img pair]: Y,N = Y
-o Output Directory, e.g. '/tmp' (if unspecified, source directory is used)
-p Protocol in filename [filename.dcm -> TFE_T1.nii]: Y,N = Y
-r Reorient image to nearest orthogonal: Y,N
-s SPM2/Analyze not SPM5/NIfTI [ignored if '-n y']: Y,N = N
-v Convert every image in the directory: Y,N = Y
-x Reorient and crop 3D NIfTI images: Y,N = N
You can also set defaults by editing /home/michael/.dcm2nii/dcm2nii.ini
EXAMPLES
dcm2nii -a y /home/joe/Documents/dcm/IM_0116
AUTHOR
dcm2nii was written by Chris Rorden.
This manual page was written by Michael Hanke <michael.hanke@gmail.com>, for the Debian project (but may be used by others).
SEE ALSO
mricron(1)
MRIcron Homepage: http://www.cabiatl.com/mricro/mricron/
Michael Hanke April 2010 DCM2NII(1)