I want to convert images from .img to .nii.gz using the function fslchfiletype.
These images are stored in Controls and Patients folders, each one of this folders have several folders belonging to each one of the individuals, like C01, C02, , etc. Specifically, each one of the individuals has the .img files inside a folder called rs_roi, which is inside another folder called ROIS2. This is what I have:
DIR="/media/Roy"; cd "$DIR/Analysis"
for group in Controls Patients; do
for case in $group; do
mkdir $DIR/Analysis/$group/$case/Cortical_masks
for file in $DIR/Analysis/$group/$case/ROIS2/rs_roi/.img; do
fslchfiletype NIFTI_GZ "$file"
done;
done;
done;
Notice how I also want to create a folder called Cortiical_maks inside each and one of the individuals.
This gives me the next error:
mkdir: cannot create directory ´media/Roy/Analysis/Controls/Controls/Cortical_masks´: No such file or directory.
Cannot open volume media/Roy/Analysis/Controls/Controls/ROIS2/rs_roi/ for reading!
mkdir: cannot create directory ´media/Roy/Analysis/Patients/Patients/Cortical_masks´: No such file or directory.
Cannot open volume media/Roy/Analysis/Patients/Patients/ROIS2/rs_roi/ for reading!
It´s iterating two times the Controls Patients folder: Control/Control. Maybe the problem is here for case in $group; do? Thx
Once you have your directory name assigned to a variable, you have to glob the directory to get its contents. Otherwise, as you saw, $group is not expanded, and you're only looping over that single term itself.
You might also like to check that each entry is indeed a directory before you traverse into it.
for case in $group/*; do
[ -d $case ] || continue
mkdir $DIR/Analysis/$group/$case/Cortical_masks
for file in $DIR/Analysis/$group/$case/ROIS2/rs_roi/.img; do
fslchfiletype NIFTI_GZ "$file"
done;
done;
You should probably also quote your variables in more places, unless you are sure they don't need quoting. I always lint my scripts with shellcheck to get that kind of advice.
I made a small change to #Noah answer, this script works fine:
for group in Controls Patients; do
for case in $group/*; do
[ -d $case ] || continue
mkdir $DIR/Analysis/$case/Cortical_masks
for file in $DIR/Analysis/$case/ROIS2/rs_roi/*.img; do
fslchfiletype NIFTI_GZ "$file"
done;
done;
done;
I deleted $group in both paths, and added * in *.img which i forgot.
Related
I've done a small amount of bash scripting. Mostly modifying a script to my needs.
On this one I am stumped.
I need a script that will read a sub-folder name inside a folder and make a numbered list of folders based on that sub-folder name.
Example:
I make a folder named “Pictures”.
Then inside I make a sub-folder named “picture-set”
I want a script to see the existing sub-folder name (picture-set) and make 10 more folders with sequential numbers appended to the end of the folder names.
ex:
folder is: Pictures
sub-folder is: picture-set
want to create:
“picture-set-01”
“picture-set-02”
“picture-set-03”
and so forth up to 10. Or a number specified in the script.
The folder structure would look like this:
/home/Pictures/picture-set
/home/Pictures/picture-set-01
/home/Pictures/picture-set-02
/home/Pictures/picture-set-03
... and so on
I am unable to tell the script how to find the base folder name to make additional folders.
ie: “picture-set”
or a better option:
Would be to create a folder and then create a set of numbered sub-folders based on the parent folder name.
ex:
/home/Songs - would become:
/home/Songs/Songs-001
/home/Songs/Songs-002
/home/Songs/Songs-003
and so on.
Please pardon my bad formatting... this is my first time asking a question on a forum such as this. Any links or pointers as to proper formatting is welcome.
Thanks for the help.
Bash has a parameter expansion you can use to generate folder names as arguments to the mkdir command:
#!/usr/bin/env bash
# Creates all directories up to 10
mkdir -p -- /home/Songs/Songs-{001..010}
This method is not very flexible if you need to dinamically change the range of numbers to generate using variables.
So you may use a Bash for loop and print format the names with desired number of digits and create each directory in the loop:
#!/usr/bin/env bash
start_index=1
end_index=10
for ((i=start_index; i<=end_index; i++)); do
# format a dirpath with the 3-digits index
printf -v dirpath '/home/Songs/Songs-%03d' $i
mkdir -p -- "$dirpath"
done
# Prerequisite:
mkdir Pictures
cd Pictures
# Your script:
min=1
max=12
name="$(basename "$(realpath .)")"
for num in $(seq -w $min $max); do mkdir "$name-$num"; done
# Result
ls
Pictures-01 Pictures-03 Pictures-05 Pictures-07 Pictures-09 Pictures-11
Pictures-02 Pictures-04 Pictures-06 Pictures-08 Pictures-10 Pictures-12
I have two folders: control and patients both with several folders inside, belonging to one individual each.
I want to do two things:
Create inside the folder for each individual a new folder called cortical_maks and inside that one, three more, called accumebens, putamen, caudate
Inside each individual folder, there are images in img format I want to convert to nii.gz using the funtion fslchfiletype.
This is what I have so far:
DIR="/media/Roy"; cd "$DIR/Analysis"
for group in Controls Patients; do
for case in $group/*; do
[ -d $case ] || continue #if its not a folder
mkdir $DIR/Analysis/$case/Cortical_masks && cd $_
mkdir accumbens putamen caudate
for file in $DIR/Analysis/$case/ROIS2/rs_roi/*.img; do
fslchfiletype NIFTI_GZ "$file"
done;
done;
done;
There are two problems with this code.
The second time you run it, the folder cortical masks is created in the main folders, that is controls and patients, that is, outside the folder it´s supposed to work.
Also, it just converts img to niig.gz for one folder at a time. First time you execute the script, converts imgs for the folder belonging to the first individual, etc
Question 01 :
The second time you run it, the folder cortical masks is created in the main folders, that is controls and patients. I want it in a way that doesn´t create new folders if there is already one with the same name.
I suggest you to use an if loop to verify if the folder cortical_mask exist before to run your code :
#check if the folder exist, if yes = true so we add ! caracter to have the opposite
if [ ! -d "$DIR/Analysis/$case/Cortical_masks" ]
then
#Your code
fi
Question 02 :
Also, it just converts img to niig.gz for one folder at a time. First time you execute the script, converts imgs for the folder belonging to the first individual, etc
If you want to do two actions in the same time, why do you not create two bash scripts and execute them simulteanously ? Or, you can automate them by creating a process in your OS which will execute scripts for you.
This has to be a duplicate but I have read and tried at least a dozen of Q&As here on SO, and I cannot get any of them working for my case.
Really hope this won't result in downvotes because of it.
So I'm on Windows (10) and have a Bash terminal that I want to use for my task. The MINGW64 one I downloaded when I started working with Git.
I would prefer the solution with this program, but will be perfectly happy with one in Command Prompt Terminal or even PowerShell.
I created a TemplateApp which is in C:\Apps\TemplateApp folder which has multiple folders and subfolders named TemplateApp or TemplateApp.something as well as a lot of files that have TemplateApp as a part of their name.
Could be:
TemplateApp.ext
TemplateApp.something.ext
something.TemplateApp.something.ext
Then I copied the uppermost folder to C:\Apps\TemplateApp - Copy and in turn renamed it to C:\Apps\ProductionApplication.
Now for the love of whomever, I cannot make any of the scripts I found on SO to work for my case, ie. to rename all the above mentioned files and folders by replacing TemplateApp with ProductionApplication.
Here is a bash function I wrote that I think does very much like what you are wanting to do.
function func_CreateSourceAndDestination() {
#
for (( i = 0 ; i < ${#files_syncSource[#]} ; i++ )) ; do
files_syncDestination[${i}]="${files_syncSource[${i}]#${directory_MusicLibraryRoot_source}}"
file_destinationPath="$( dirname -- "${directory_PMPRoot_destination}${files_syncDestination[${i}]}" )"
if [ ! -d "${file_destinationPath}" ] ; then
mkdir -p "${file_destinationPath}"
fi
rsync -rltDvPmz "${files_syncSource[${i}]}" "${directory_PMPRoot_destination}${files_syncDestination[${i}]}"
done
}
In my case I'm feeding into rsync for a source and a destination. I'm pulling all the file paths from an array that has been split into path segments. I have to make certain character substitutions for FAT and NTFS file systems. I do this recursively.
files_syncDestination[${i}]="${files_syncDestination[${i}]//\:/__}"
That's the magic. I load a new array with the character substituted. You could do the same with a loaded variable including your phrases for change.
files_syncDestination[${i}]="${files_syncDestination[${i}]//${targetPhrase}/${subPhrase}}"
After that change in the function, you could use rsync or cp or mv as you prefer to go from your source array to your destination array.
(The double-slash in the substitution makes the substitution global.)
my function is supposed to list all running processes and store them to process.id and if process.id exists, it should rename it to the current date with .id at the end of it, and then move it to the /logs directory. i think i have the mv and rename part working but it doesnt seem to save all of the processes to the file. do i have a syntax error on that part?
function processsaver()
{
if [ -r "process.id" ]; then
mv "process.id" logs/$(date +%d-%m-%y).id
ps -e > /process.id
fi
}
process.id and /process.id are not the same path. You probably wanted process.id or ./process.id in both places, since this kind of information really should not be in the filesystem root.
I'm not very good in shell scripting and would like to ask you some question about looping of files big dataset: in my example I have alot of files with the common .pdb extension in the work dir. I need to loop all of them and i) to print name (w.o pdb extension) of each looped file and make some operation after this. E.g I need to make new dir for EACH file outside of the workdir with the name of each file and copy this file to that dir. Below you can see example of my code which are not worked- it's didn't show me the name of the file and didn't create folder for each of them. Please correct it and show me where I was wrong
#!/bin/bash
# set the work dir
receptors=./Receptors
for pdb in $receptors
do
filename=$(basename "$pdb")
echo "Processing of $filename file"
cd ..
mkdir ./docking_$filename
done
Many thanks for help,
Gleb
If all your files are contained within the .Repectors folder, you can loop each of them like so:
#!/bin/bash
for pdb in ./Receptors/*.pdb ; do
filename=$(basename "$pdb")
filenamenoextention=${filename/.pdb/}
mkdir "../docking_${filenamenoextention}"
done
Btw:
filenamenoextention=${filename/.pdb/}
Does a search replace in the variable $pdb. The syntax is ${myvariable/FOO/BAR}, and replaces all "FOO" substrings in $myvariable with "BAR". In your case it replaces ".pdb" with nothing, effectively removing it.
Alternatively, and safer (in case $filename contains multiple ".pdb"-substrings) is to remove the last four characters, like so: filenamenoextention=${filename:0:-4}
The syntax here is ${myvariable:s:e} where s and e correspond to numbers for the start and end index (not inclusive). It also let's you use negative numbers, which are offsets from the end. In other words: ${filename:0:-4} says: extract the substring from $filename starting from index 0, until you reach fourth-to-the-last character.
A few problems you have had with your script:
for pdb in ./Receptors loops only "./Receptors", and not each of the files within the folder.
When you change to parent directory (cd ..), you do so for the current shell session. This means that you keep going to the parent directory each time. Instead, you can specify the parent directory in the mkdir call. E.g mkdir ../thedir
You're looping over a one-item list, I think what you wanted to get is the list of the content of ./Receptors:
...
for pdb in $receptors/*
...
to list only file with .pdb extension use $receptors/*.pdb
So instead of just giving the path in for loop, give this:
for pdb in $receptors/*.pdb
To remove the extension :
set the variable ext to the extension you want to remove and using shell expansion operator "%" remove the extension from your filename eg:
ext=.pdb
filename=${filename%${ext}}
You can create the new directory without changing your current directory:
So to create a directory outside your current directory use the following command
mkdir ../docking_$filename
And to copy the file in the new directory use cp command
After correction
Your script should look like:
receptors=./Receptors
ext=.pdb
for pdb in $receptors/*.pdb
do
filename=$(basename "$pdb")
filename=${filename%${ext}}
echo "Processing of $filename file"
mkdir ../docking_$filename
cp $pdb ../docking_$filename
done