Direct recursive shell script output to each subdirectory, not parent directory

Question

I'm processing a batch of subjects data recursively, calling the script within the parent directory.

For example, I have the parent directory:

/home/subjects

and the subdirectories which contain the data:

/home/subjects/0393
/home/subjects/0389
/home/subjects/9920 (Around 250 subjects)

Each file in each subdirectory has the file extension ".nii". I have composed a code, which calls a number of commands from a neuroscience program, searching for that particular file extension as the input. The input to the first command "fslroi" is the .nii file ($file), while the output file of that command is "rawdata.nii". As you can see the output from one command, is the input to the next etc

for file in $(find ./ -name "*.nii")
do
fslroi $file rawdata.nii 0 33
gunzip rawdata.nii.gz -f
fslroi rawdata.nii rawnodif 0 1
bet rawnodif rawnodif_brain -m -g 0.2 -f 0.3
fslmaths rawnodif -mas rawnodif_brain_mask rawnodif_brain
gunzip rawnodif_brain_mask.nii.gz -f
done

However, this code is inadequate as I am unable to save the output into the particular subdirectory. Thus, as I am processing several subjects the code will not work as everything is being saved to the parent directory.

Could someone please be able to give me any hints to how I can modify the code to save the output according to the input ".nii" file?

Answer 1

You want to use dirname $file to get the directory name of your input file and prepend that to the output filename.

for file in $(find ./ -name "*.nii")
do
rawdata = $(dirname $file)/rawdata.nii
fslroi $file $rawdata 0 33
gunzip $rawdata.gz -f
fslroi $rawdata rawnodif 0 1
bet rawnodif rawnodif_brain -m -g 0.2 -f 0.3
fslmaths rawnodif -mas rawnodif_brain_mask rawnodif_brain
gunzip rawnodif_brain_mask.nii.gz -f
done

It is unclear which of the rawdata are actual command arguments or if all are filenames. Same with rawnodif_brain_mask which you might need to adapt in the same way.

Answer 2

Thank you, here is the final script. Note the $ denotes a filename, whilst the rest are commands or arguments.

#!/bin/bash

for file in $(find ./ -name "*.nii")
do
rawdata=$(dirname $file)/rawdata.nii.gz
rawnodif=$(dirname $file)/rawnodif.nii.gz
rawnodif_brain=$(dirname $file)/rawnodif_brain.nii.gz
rawnodif_brain_mask=$(dirname $file)/rawnodif_brain.nii.gz
fslroi $file $rawdata 0 33
fslroi $rawdata $rawnodif 0 1
gunzip $rawdata -f
bet $rawnodif $rawnodif_brain -m -g 0.2 -f 0.3
fslmaths $rawnodif -mas $rawnodif_brain_mask $rawnodif_brain
gunzip $rawnodif_brain_mask -f
done