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horosproject / horos

Horos™ is a free, open source medical image viewer. The goal of the Horos Project is to develop a fully functional, 64-bit medical image viewer for OS X. Horos is based upon OsiriX and other open source medical imaging libraries. Horos is made freely available under the GNU Lesser General Public License, Version 3 (LGPL-3.0). Horos is linked against the Grok JPEG 2000 library, for fast viewing of JPEG 2000 images. This library is licensed under the terms of the GNU Affero General Public License.
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Export patients in Bulk using Python #708

Open sulaimanvesal opened 2 years ago

sulaimanvesal commented 2 years ago

Hi,

Is there any python API for Horos that could allow us export Patient Dicom (full series) using Python? For example I have around 500 patients that I need to export all the DICOM series based on MRNs. Manually, it takes quite sometime and I wanted to automate this process somehow?

I would appreciate any guide on this. I looked for other solutions like pynetdicom? but that wasn't really clear approach.

Best,

sorenchr2011 commented 2 years ago

Hi, There's pyosirix but I have no personal experience with it. If you need all series exported for a subset of your MRNs then you are trying to avoid making 500 selections or where is it you wish to save time? I could see the need for automation if you were after series only but if you want all series for an MRN is there that much gained in automation? In any case, I have a plugin i use for this that i am happy to share if you don't find other solutions. Soren

On Mon, Jul 18, 2022, 22:57 Sulaiman Vesal @.***> wrote:

Hi,

Is there any python API for Horos that could allow us export Patient Dicom (full series) using Python? For example I have around 500 patients that I need to export all the DICOM series based on MRNs. Manually, it takes quite sometime and I wanted to automate this process somehow?

I would appreciate any guide on this. I looked for other solutions like pynetdicom? but that wasn't really clear approach.

Best,

— Reply to this email directly, view it on GitHub https://github.com/horosproject/horos/issues/708, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAHBDDIJ4BR72E2QKGQPFLDVUXAKFANCNFSM535UEHWA . You are receiving this because you are subscribed to this thread.Message ID: @.***>

sulaimanvesal commented 2 years ago

Hi Soren,

Thank you for prompt response.

I could see the need for automation if you were after series only but if you want all series for an MRN is there that much gained in automation? Your are right, however in horos I need to search each MRN and pull it out from entire cohort. This is very manual and takes so much time. I thought, having all MRNs as a list and just feed it to a Python API and call Horos to retrieve and save them into disk without searching manually.

It would be great if you could share the plugin.

best, Sulaiman

ryanapfel commented 2 years ago

A bit more of a hack is to run a python script across your entire database folder using pydicom.

jlalden commented 1 year ago

Hi, Sulaiman - Did you ever find a solution to this? I am currently in a similar situation...I'd like to use Python to export a large number of studies from Horos to another recipient, and am looking for something that would accomplish that. Many thanks, John