AFNI Message Board

Dear AFNI users-

We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:

https://discuss.afni.nimh.nih.gov

Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.

The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.

Sincerely, AFNI HQ

History of AFNI updates  

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August 20, 2021 02:58PM
Hi Philipp,

There are a few things to note here.

1. You seem to be on a mac, which rarely kills a program that is allocating "too much" memory. Rather, it adds virtual swap space and just takes. for. ever. (give or take 3 weeks).

2. There are 2360 time points across those 3 runs? That is quite a few time points. What polort is 3dDeconvolve using?

3. Worse, there are 1482 baseline regressors. That is scary.

Oooooooohhhh! You are using large-scale bandpassing in a normal linear regression model. That is why there are so many baseline regressors, and part of why it is taking so long.

Since this is a task analysis, try it without "-regress_bandpass 0.01 0.2". With so many time points, I am not positive whether it will work on that laptop, but removing almost 1500 regressors will help reduce the memory requirement (and we tend to prefer not bandpassing anyway).

Also, add -regress_compute_fitts to the command.
Instead of having 3dDeconvolve compute that, it will be done with 3dcalc (after the regression is done). That will save quite a bit of memory for 3dDeconvolve.

Also, since you are running out of memory, consider closing any MS Office applications, or anything else that might use a lot of RAM.

Hopefully some of that will help.

- rick
Subject Author Posted

AFNI_proc.py - A faulty warped brain Attachments

Philipp August 17, 2021 10:14AM

Re: AFNI_proc.py - A faulty warped brain

ptaylor August 17, 2021 01:48PM

Re: AFNI_proc.py - A faulty warped brain

Philipp August 18, 2021 05:51AM

Re: AFNI_proc.py - A faulty warped brain

rick reynolds August 18, 2021 10:39AM

Re: AFNI_proc.py - A faulty warped brain Attachments

ptaylor August 18, 2021 07:59PM

Re: AFNI_proc.py - A faulty warped brain

ptaylor August 18, 2021 08:20PM

Re: AFNI_proc.py - A faulty warped brain

Philipp August 19, 2021 08:41AM

Re: AFNI_proc.py - A faulty warped brain

rick reynolds August 19, 2021 09:05AM

Re: AFNI_proc.py - A faulty warped brain Attachments

Philipp August 20, 2021 11:26AM

Re: AFNI_proc.py - A faulty warped brain

rick reynolds August 20, 2021 02:58PM

Re: AFNI_proc.py - A faulty warped brain

ptaylor August 20, 2021 03:19PM

Re: AFNI_proc.py - A faulty warped brain

Philipp August 21, 2021 03:24AM

Re: AFNI_proc.py - A faulty warped brain

rick reynolds August 21, 2021 06:59PM