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Re: [shapeworks-users] Query on shapework


Chronological Thread 
  • From: Shireen Elhabian <shireen@sci.utah.edu>
  • To: Kazi Hasan Ibn Arif <1605034@ugrad.cse.buet.ac.bd>
  • Cc: Shireen Elhabian <shireen@sci.utah.edu>, Jainta Paul <1605022@ugrad.cse.buet.ac.bd>, Mursheda Tasnim <1605095@ugrad.cse.buet.ac.bd>, shapeworks-users@sci.utah.edu
  • Subject: Re: [shapeworks-users] Query on shapework
  • Date: Mon, 7 Jun 2021 08:56:13 -0600
  • Ironport-sdr: C7YfwyHDTmdw/hCVgSw3hONotV9LxZ4FQvaNZEWcoG4yjhK+gBnD6CcgvBeYvLnAOUcrAff9LG akDSfcm/WQsR+I+iE6iLO52JE+w6zL7AzoCs7IzwphCukcWmhhaeTK6c3Jf7RERVe6xxm8nZqU UNLlu5lwDep6rlUvXFYKI6Ke29m1esOWjIQHV/xxrYQmTLnHwH3LgfKQBy/S2k9QgLyqw1lkD1 CEYowfAv49s/DgbAyiDd50AOQOhQBJ/Rf/NkgOX3/6ZGDsHL3zF2z49961b1mTSpapDfqNGfzf ZIs=
@Kazi, we are working on provide exemplar notebooks that can work on remote servers as Collab. As of now, the only part of ShapeWorks tools that require GPU is DeepSSM. Is this what you would like to use? Otherwise, ShapeWorks can work on CPU and with meshes 8GB should be fine unless you a large-sized cohort. Can you provide more details? Also, could you please post your questions on the discussion forum to allow all the dev team to participate in the discussion and help you out?

thanks and best regards
Shireen


------------------------------------------
Shireen Elhabian, M.Sc., Ph.D.
Research Assistant Professor, School of Computing
Research Computer Scientist, Scientific Computing and Imaging Institute
University of Utah
WEB 2815
72 Central Campus Drive, Salt Lake City, UT, 84112
Phone (801) 587-3206
Fax (801) 585-6513
Home Page: http://www.sci.utah.edu/~shireen

On Jun 7, 2021, at 8:42 AM, Kazi Hasan Ibn Arif <1605034@ugrad.cse.buet.ac.bd> wrote:

Dear,

Thanks for replying. I really appreciate your effort. The documentation itself is very lucid and self explanatory but I am facing some problem to move forward with “PyTorch GPU support for ShapeWorks"


Is there any way I can run this on Colab? My laptop is Macbook M1 8GB, so I can not connect CUDA as this has different kinds of GPU architecture. I went  through the forum but haven’t found any answer to this. So I was wondering whetherr  I may use shapeworks on google colab. 

Regards. 


--------------------------------------------------------------------

Kazi Hasan Ibn Arif
Undergrad Student
Dept of Computer Science and Engineering
Bangladesh University of Engineering and Technology
Dhaka, Bangladesh

On 1 Jun, 2021 9:39 PM +0600, Shireen Elhabian <shireen@sci.utah.edu>, wrote:
Hi Kazi,

Thanks for reaching out and glad to know your interest in ShapeWorks. We have recently added mesh support to ShapeWorks and Studio. This significantly helps with reducing the memory footprint.

I think the best course to help you out with your use case is to post your questions on the discussion forum (link below). 
https://shapeworks.discourse.group

To get you started, here is some documentations

Regards
Shireen


------------------------------------------
Shireen Elhabian, M.Sc., Ph.D.
Research Assistant Professor, School of Computing
Research Computer Scientist, Scientific Computing and Imaging Institute
University of Utah
WEB 2815
72 Central Campus Drive, Salt Lake City, UT, 84112
Phone (801) 587-3206
Fax (801) 585-6513
Home Page: http://www.sci.utah.edu/~shireen
On May 31, 2021, at 11:44 AM, Kazi Hasan Ibn Arif <1605034@ugrad.cse.buet.ac.bd> wrote:

Dear

I and my parters are working on a research project on bone image analysis using ShapeWork. Is there any way to run codes from a low end  (8GB ram) machine? The problem is, when I try to run segmentation for femur dataset in Jupyter notebook, I am running out of memory.

How can I proceed?

Thank you

--------------------------------------------------------------------

Kazi Hasan Ibn Arif
Undergrad student
Level-4 Term-1
Bangladesh University of Engineering and Technology
Dhaka, Bangladesh




  • Re: [shapeworks-users] Query on shapework, Shireen Elhabian, 06/07/2021

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