How to make a script that copies files from different subject folders?
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I'm having trouble setting up a script that copies and converts files. What I basically want is a script that takes a subject e.g.
folder/subjects/subject_name/mri/norm.mgz
copies this file into
folder/investigation_folder/fs_norms/subject_name/
and converts the norm.mgz to norm.nii using mri_convert, and does this with +300 subjects (in the subjects folder).
This should be fairly simple... Can anybody help me out here?
I'm a big newb! This is a example of what i would like to do - with a single subject:
mkdir /mnt/projects/Project_folder/thalamic_subnuclei/fs_norms/gXXX/
cp /mnt/projects/Project_folder/subjects/gXXX/mri/norm.mgz /mnt/projects/Project_folder/thalamic_subnuclei/fs_norms/gXXX/
mri_convert mnt/projects/Project_folder/thalamic_subnuclei/fs_norms/gXXX/norm.mgz mnt/projects/Project_folder/thalamic_subnuclei/fs_norms/gXXX/norm.nii
All my subjects are called g followed by 3-4 numbers. Now I need to set up a loop that does this with the +300 subjects in the /mnt/projects/Project_folder/subjects/ folder.
bash scripts
edited Apr 24 at 12:28
pa4080
12k52255
asked Apr 24 at 11:19
Silas Nielsen
83
add a comment |Â
up vote
1
down vote
favorite
I'm having trouble setting up a script that copies and converts files. What I basically want is a script that takes a subject e.g.
folder/subjects/subject_name/mri/norm.mgz
copies this file into
folder/investigation_folder/fs_norms/subject_name/
and converts the norm.mgz to norm.nii using mri_convert, and does this with +300 subjects (in the subjects folder).
This should be fairly simple... Can anybody help me out here?
I'm a big newb! This is a example of what i would like to do - with a single subject:
mkdir /mnt/projects/Project_folder/thalamic_subnuclei/fs_norms/gXXX/
cp /mnt/projects/Project_folder/subjects/gXXX/mri/norm.mgz /mnt/projects/Project_folder/thalamic_subnuclei/fs_norms/gXXX/
mri_convert mnt/projects/Project_folder/thalamic_subnuclei/fs_norms/gXXX/norm.mgz mnt/projects/Project_folder/thalamic_subnuclei/fs_norms/gXXX/norm.nii
All my subjects are called g followed by 3-4 numbers. Now I need to set up a loop that does this with the +300 subjects in the /mnt/projects/Project_folder/subjects/ folder.
bash scripts
edited Apr 24 at 12:28
pa4080
12k52255
asked Apr 24 at 11:19
Silas Nielsen
83
2
You are probably right about the simplicity. Will you edit your question snow us how far you've gotten and where you're stuck? A script is a simple list of commands. Write down each command when performing the steps on one file. Then put the commands in a loop. If you get stuck, we'll help you to fix your script, but we need to know where you are stuck.
– L. D. James
Apr 24 at 11:34
See surfer.nmr.mgh.harvard.edu/fswiki/mri_convert formri_convert's syntax.
– dessert
Apr 24 at 13:28
add a comment |Â
up vote
1
down vote
favorite
up vote
1
down vote
favorite
I'm having trouble setting up a script that copies and converts files. What I basically want is a script that takes a subject e.g.
folder/subjects/subject_name/mri/norm.mgz
copies this file into
folder/investigation_folder/fs_norms/subject_name/
and converts the norm.mgz to norm.nii using mri_convert, and does this with +300 subjects (in the subjects folder).
This should be fairly simple... Can anybody help me out here?
I'm a big newb! This is a example of what i would like to do - with a single subject:
mkdir /mnt/projects/Project_folder/thalamic_subnuclei/fs_norms/gXXX/
cp /mnt/projects/Project_folder/subjects/gXXX/mri/norm.mgz /mnt/projects/Project_folder/thalamic_subnuclei/fs_norms/gXXX/
mri_convert mnt/projects/Project_folder/thalamic_subnuclei/fs_norms/gXXX/norm.mgz mnt/projects/Project_folder/thalamic_subnuclei/fs_norms/gXXX/norm.nii
All my subjects are called g followed by 3-4 numbers. Now I need to set up a loop that does this with the +300 subjects in the /mnt/projects/Project_folder/subjects/ folder.
bash scripts
edited Apr 24 at 12:28
pa4080
12k52255
asked Apr 24 at 11:19
Silas Nielsen
83
I'm having trouble setting up a script that copies and converts files. What I basically want is a script that takes a subject e.g.
folder/subjects/subject_name/mri/norm.mgz
copies this file into
folder/investigation_folder/fs_norms/subject_name/
and converts the norm.mgz to norm.nii using mri_convert, and does this with +300 subjects (in the subjects folder).
This should be fairly simple... Can anybody help me out here?
I'm a big newb! This is a example of what i would like to do - with a single subject:
mkdir /mnt/projects/Project_folder/thalamic_subnuclei/fs_norms/gXXX/
cp /mnt/projects/Project_folder/subjects/gXXX/mri/norm.mgz /mnt/projects/Project_folder/thalamic_subnuclei/fs_norms/gXXX/
mri_convert mnt/projects/Project_folder/thalamic_subnuclei/fs_norms/gXXX/norm.mgz mnt/projects/Project_folder/thalamic_subnuclei/fs_norms/gXXX/norm.nii
All my subjects are called g followed by 3-4 numbers. Now I need to set up a loop that does this with the +300 subjects in the /mnt/projects/Project_folder/subjects/ folder.
bash scripts
edited Apr 24 at 12:28
pa4080
12k52255
asked Apr 24 at 11:19
Silas Nielsen
83
edited Apr 24 at 12:28
pa4080
12k52255
edited Apr 24 at 12:28
pa4080
12k52255
edited Apr 24 at 12:28
pa4080
12k52255
12k52255
asked Apr 24 at 11:19
Silas Nielsen
83
asked Apr 24 at 11:19
Silas Nielsen
83
asked Apr 24 at 11:19
Silas Nielsen
83
83
2
You are probably right about the simplicity. Will you edit your question snow us how far you've gotten and where you're stuck? A script is a simple list of commands. Write down each command when performing the steps on one file. Then put the commands in a loop. If you get stuck, we'll help you to fix your script, but we need to know where you are stuck.
– L. D. James
Apr 24 at 11:34
See surfer.nmr.mgh.harvard.edu/fswiki/mri_convert formri_convert's syntax.
– dessert
Apr 24 at 13:28
add a comment |Â
2
You are probably right about the simplicity. Will you edit your question snow us how far you've gotten and where you're stuck? A script is a simple list of commands. Write down each command when performing the steps on one file. Then put the commands in a loop. If you get stuck, we'll help you to fix your script, but we need to know where you are stuck.
– L. D. James
Apr 24 at 11:34
See surfer.nmr.mgh.harvard.edu/fswiki/mri_convert formri_convert's syntax.
– dessert
Apr 24 at 13:28
2
2
You are probably right about the simplicity. Will you edit your question snow us how far you've gotten and where you're stuck? A script is a simple list of commands. Write down each command when performing the steps on one file. Then put the commands in a loop. If you get stuck, we'll help you to fix your script, but we need to know where you are stuck.
– L. D. James
Apr 24 at 11:34
You are probably right about the simplicity. Will you edit your question snow us how far you've gotten and where you're stuck? A script is a simple list of commands. Write down each command when performing the steps on one file. Then put the commands in a loop. If you get stuck, we'll help you to fix your script, but we need to know where you are stuck.
– L. D. James
Apr 24 at 11:34
See surfer.nmr.mgh.harvard.edu/fswiki/mri_convert for
mri_convert's syntax.– dessert
Apr 24 at 13:28
See surfer.nmr.mgh.harvard.edu/fswiki/mri_convert for
mri_convert's syntax.– dessert
Apr 24 at 13:28
add a comment |Â
1 Answer
1
active
oldest
votes
up vote
2
down vote
accepted
Here is an example how the FOR loop can be applied within a bash script to solve this task:
#!/bin/bash
# Execute do-done inner part for each "item" under "folder/subjects/"
for subject in folder/subjects/*
do
# Check whether the source file exists
if [[ -f $subject/mri/norm.mgz ]]
then
# $subject##*/ will cut the parent path from the value of the variable '$subject'
echo "Processing: $subject##*/"
# Create the new subject directory
mkdir -p "folder/investigation_folder/fs_norms/$subject##*/"
# Copy the .mgz file into the new directory
cp "$subject/mri/norm.mgz" "folder/investigation_folder/fs_norms/$subject##*//"
# Do the conversion to .nii (I'm not sure this is the correct syntax of mri_convert that you are using)
mri_convert "folder/investigation_folder/fs_norms/$subject##*//norm.mgz" "folder/investigation_folder/fs_norms/$subject##*//norm.nii"
fi
done
edited Apr 24 at 13:25
dessert
19.8k55594
answered Apr 24 at 12:00
pa4080
12k52255
add a comment |Â
1 Answer
1
active
oldest
votes
1 Answer
1
active
oldest
votes
active
oldest
votes
active
oldest
votes
up vote
2
down vote
accepted
Here is an example how the FOR loop can be applied within a bash script to solve this task:
#!/bin/bash
# Execute do-done inner part for each "item" under "folder/subjects/"
for subject in folder/subjects/*
do
# Check whether the source file exists
if [[ -f $subject/mri/norm.mgz ]]
then
# $subject##*/ will cut the parent path from the value of the variable '$subject'
echo "Processing: $subject##*/"
# Create the new subject directory
mkdir -p "folder/investigation_folder/fs_norms/$subject##*/"
# Copy the .mgz file into the new directory
cp "$subject/mri/norm.mgz" "folder/investigation_folder/fs_norms/$subject##*//"
# Do the conversion to .nii (I'm not sure this is the correct syntax of mri_convert that you are using)
mri_convert "folder/investigation_folder/fs_norms/$subject##*//norm.mgz" "folder/investigation_folder/fs_norms/$subject##*//norm.nii"
fi
done
edited Apr 24 at 13:25
dessert
19.8k55594
answered Apr 24 at 12:00
pa4080
12k52255
add a comment |Â
up vote
2
down vote
accepted
Here is an example how the FOR loop can be applied within a bash script to solve this task:
#!/bin/bash
# Execute do-done inner part for each "item" under "folder/subjects/"
for subject in folder/subjects/*
do
# Check whether the source file exists
if [[ -f $subject/mri/norm.mgz ]]
then
# $subject##*/ will cut the parent path from the value of the variable '$subject'
echo "Processing: $subject##*/"
# Create the new subject directory
mkdir -p "folder/investigation_folder/fs_norms/$subject##*/"
# Copy the .mgz file into the new directory
cp "$subject/mri/norm.mgz" "folder/investigation_folder/fs_norms/$subject##*//"
# Do the conversion to .nii (I'm not sure this is the correct syntax of mri_convert that you are using)
mri_convert "folder/investigation_folder/fs_norms/$subject##*//norm.mgz" "folder/investigation_folder/fs_norms/$subject##*//norm.nii"
fi
done
edited Apr 24 at 13:25
dessert
19.8k55594
answered Apr 24 at 12:00
pa4080
12k52255
add a comment |Â
up vote
2
down vote
accepted
up vote
2
down vote
accepted
Here is an example how the FOR loop can be applied within a bash script to solve this task:
#!/bin/bash
# Execute do-done inner part for each "item" under "folder/subjects/"
for subject in folder/subjects/*
do
# Check whether the source file exists
if [[ -f $subject/mri/norm.mgz ]]
then
# $subject##*/ will cut the parent path from the value of the variable '$subject'
echo "Processing: $subject##*/"
# Create the new subject directory
mkdir -p "folder/investigation_folder/fs_norms/$subject##*/"
# Copy the .mgz file into the new directory
cp "$subject/mri/norm.mgz" "folder/investigation_folder/fs_norms/$subject##*//"
# Do the conversion to .nii (I'm not sure this is the correct syntax of mri_convert that you are using)
mri_convert "folder/investigation_folder/fs_norms/$subject##*//norm.mgz" "folder/investigation_folder/fs_norms/$subject##*//norm.nii"
fi
done
edited Apr 24 at 13:25
dessert
19.8k55594
answered Apr 24 at 12:00
pa4080
12k52255
Here is an example how the FOR loop can be applied within a bash script to solve this task:
#!/bin/bash
# Execute do-done inner part for each "item" under "folder/subjects/"
for subject in folder/subjects/*
do
# Check whether the source file exists
if [[ -f $subject/mri/norm.mgz ]]
then
# $subject##*/ will cut the parent path from the value of the variable '$subject'
echo "Processing: $subject##*/"
# Create the new subject directory
mkdir -p "folder/investigation_folder/fs_norms/$subject##*/"
# Copy the .mgz file into the new directory
cp "$subject/mri/norm.mgz" "folder/investigation_folder/fs_norms/$subject##*//"
# Do the conversion to .nii (I'm not sure this is the correct syntax of mri_convert that you are using)
mri_convert "folder/investigation_folder/fs_norms/$subject##*//norm.mgz" "folder/investigation_folder/fs_norms/$subject##*//norm.nii"
fi
done
edited Apr 24 at 13:25
dessert
19.8k55594
answered Apr 24 at 12:00
pa4080
12k52255
edited Apr 24 at 13:25
dessert
19.8k55594
edited Apr 24 at 13:25
dessert
19.8k55594
edited Apr 24 at 13:25
dessert
19.8k55594
19.8k55594
answered Apr 24 at 12:00
pa4080
12k52255
answered Apr 24 at 12:00
pa4080
12k52255
answered Apr 24 at 12:00
pa4080
12k52255
12k52255
add a comment |Â
add a comment |Â
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2
You are probably right about the simplicity. Will you edit your question snow us how far you've gotten and where you're stuck? A script is a simple list of commands. Write down each command when performing the steps on one file. Then put the commands in a loop. If you get stuck, we'll help you to fix your script, but we need to know where you are stuck.
– L. D. James
Apr 24 at 11:34
See surfer.nmr.mgh.harvard.edu/fswiki/mri_convert for
mri_convert's syntax.– dessert
Apr 24 at 13:28