Preserving initial folder structure

[jkarten95]

Hi All,

In reading the documentation, I see that I can output a newly de-identified .dcm file to a specified folder. I was wondering if there is a way to de-identify "in place" instead of sending to a new folder and thereby preserving the original folder structure? I ask because the imaging studies are kept in complex folder structures that we'd like to maintain. Thanks for any advice!

Jordan

[vsoch]

Could you show me the exact command you are running so I can take a look? There are several ways to interact with deid and I want to make sure we are discussing the same one.

[jkarten95]

Sure!

base = '/folder/with/original/study/directories'
dicom_files = list(get_files(base))

#other code

cleaned_files = replace_identifiers(dicom_files=dicom_files, deid=recipe, ids=items, save=True, overwrite=True, 
output_folder='/folder/for/new/files'). 

I am wondering if instead of stripping the .dcm files from the original location, can they be saved in their original folders? Essentially I have multiple imaging studies in one directory.

[vsoch]

@jkarten95 did you try setting the same output folder as where you already have the files, and then overwrite to True?

[vsoch]

Actually scratch that - just leave the output folder as None and set overwrite to true. See here:

deid/deid/dicom/utils.py

Line 97 in 7e7196d

if output_folder is None:

[vsoch]

Based on reading the code, that should accomplish what you want (let me know if it does not!)

[jkarten95]

That worked perfectly! Thanks for the help.

[vsoch]

Definitely! Happy to do so :)