Can I automate just importing files, changing their type, and then saving them?

Development
1

I am trying to write a Python script that imports .msg files into 3D Slicer and saves them as nii files. I’ve never automated anything and I am having a bit of a hard time understanding how to write scripts and run them. Thanks.

2

If you don’t need to do anything interactive with the files, then you probably don’t need to load them into Slicer at all. You might take a look at the slicerio python package and see if you can use that to just load and save the data formats you need.

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3

Thanks so much!!! I will check it out!

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4

I ended up using freesurfer’s mri_convert command and wrote a BASH script to loop through all the files in a directory and convert them. Here’s the code:

#!/bin/bash 

#ask user for filepath and change directory to filepath 
read -p "Enter filepath: " fp  
cd $fp 

#loop through files 
for FILE in * 
do 
        #seperate file extentsion and name 
        filepath="${fp}${FILE}" 
        filename_with_ext=$(basename $filepath) 
        filename="${filename_with_ext%.*}" 
        extension="${filename_with_ext##*.}" 

        #concatinate filename with new extension         
        ni_file="${filename}.nii" 

        #convert to nii using now seperated file name concaqtinated with .nii 
        mri_convert --in_type mgz --out_type nii ${FILE} ${ni_file} 
done 

 #switch back to home directory 
cd ~
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