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thalamicseg / hipsthomasdocker

Docker version of HIPS-THOMAS
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Stuck at the step antsRegistation #1

Open XinyuLiu1999 opened 1 year ago

XinyuLiu1999 commented 1 year ago

Hi,

I am trying to run this tool for example data. However every time I ran it, I was stuck at this step: image It takes forever and can not continue. I tried it with both MacOS and WSL and both didn't work.

Could you help resolving this? Thank you very much!

Xinyu

leRequinRomain commented 1 year ago

I have the same issue. Did you ever find a solution?

image

XinyuLiu1999 commented 1 year ago

I have the same issue. Did you ever find a solution?

image

Hi,

After communication with the author this is due to insufficient RAM, since this step would take a significant amount of memory. One solution I found for my MacOS is to turn on the Rosetta option in docker, then it can be run smoothly within 1 hour. It is also recommended to run in a Linux computer rather than from a virtual machine etc, which will limit RAM usage.

leRequinRomain commented 1 year ago

After making the post, I let the program run for a long time. It eventually completed, but was stuck at this step for about 20-30 minutes. The same behavior occurred with both example scripts. I ran the program on Windows 10 Ubuntu WSL2 with 64 GB RAM.

From: XinyuLiu1999 @.> Sent: Tuesday, September 5, 2023 9:05 AM To: thalamicseg/hipsthomasdocker @.> Cc: Holman, Ryan @.>; Comment @.> Subject: Re: [thalamicseg/hipsthomasdocker] Stuck at the step antsRegistation (Issue #1)

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I have the same issue. Did you ever find a solution?

[image]https://secure-web.cisco.com/1TBIP682Z7-g6XO20al_7Yyf9tq85VsfBKM1sJXda_bBgirb90Nf6lvTtuGg2jF_5umIxGJG7SDxGLZwBV7VBHQ9D1Zg5NeYF2lu5TNstlubNrl7psP2gTyIi7PrMWENj1hbKRAEIIndtLsX9iXzAVIO_Gv-yQaVQkjjB3RQug80O5bzUGo3rrkqbeaACd9B5aC-kr8Kp7O08rNgpc74zXoPcNtnFaJ9iMgrUExFY7e1NWoCazQyHTYozbY2TFN4ydQ8i5uyvJHiFZBmvZDi1cbWyNK3EIGG-hArnP9cCfKeZmHPzqewnsSJ3YTtGUkSaM5qHlR_vOPUjf7I9-dljKQ/https%3A%2F%2Fuser-images.githubusercontent.com%2F143903679%2F265224770-815b58ea-08e8-477f-9b65-50214e4452c9.png

Hi,

After communication with the author this is due to insufficient RAM, since this step would take a significant amount of memory. One solution I found for my MacOS is to turn on the Rosetta option in docker, then it can be run smoothly within 1 hour. It is also recommended to run in a Linux computer rather than from a virtual machine etc, which will limit RAM usage.

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anagrammarian commented 3 months ago

Yes this is the ANTS nonlinear registration step which can take anywhere from 10-30 min depending on your processor. It takes about 20 min on a cheap PC running Ubuntu and about 10 min on a ThinkStation which is more snazzy. There is an issue on Macs running Apple silicon and the fix is on the main thread (install rosetta and make sure it is enabled and make sure docker allocation of memory is increased, default is ridiculously small).

The file NULL does not exist is an ANTS warning which should not happen according to the ANTs developers but does as we are not passing real mask files (defaults to NULL). It is benign and will complete.