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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Dan
October 04, 2018 09:16PM
Hi Rick,

Thank you for your response. Correcting the last parameter in the -concat option did indeed resolve the 2nd set of warning message I was getting.

Regarding the timing files, this is related to a previous question I posted earlier (https://afni.nimh.nih.gov/afni/community/board/read.php?1,159421,159421#msg-159421), where I provided one of my timing files, which only has duration modulation:

10.15:16.78 90.12:19.79 116.94:22.43 173.97:7.11 219.81:4.58 231.41:1.58 286.55:11.17 304.75:17.96
1.02:11.35 19.4:4.85 42.13:12.0 63.16:5.61 128.22:12.11 147.36:10.15 170.42:2.35 181.8:19.86 222.31:2.82 238.48:3.67 311.72:22.09
1.03:14.16 55.54:4.05 66.63:15.91 117.45:10.59 135.08:5.05 169.68:7.57 194.14:6.99 244.7:2.8 281.33:3.94 311.82:2.92 321.76:30.74
20.38:7.09 34.51:21.36 100.33:2.37 124.36:13.71 145.09:4.81 162.5:1.82 173.35:11.78 218.0:8.48 233.51:1.72 262.39:42.91 314.33:8.67
1.02:28.95 35.0:18.26 80.74:30.0 160.28:26.33 191.64:2.73 221.25:27.31
1.03:7.51

The reason why I'm also interested in amplitude modulation is because my task involves presenting neutral and aversive images, and I worry that habituation to the aversive stimuli over the course of the experiment will attenuate the response amplitude. Assuming this logic is correct, it looks like I would need to adjust my timing files to include the AM parameter(s). In one of your responses, you provided an example of '10.15*1.83:16.78' , and the 3dDeconvolve help file provides an example of '30*5,3:12'. My question is, is there a mathematical formula or rule of thumb for determining the AM parameter(s)? Or would I be better off just focusing on duration modulation instead?

I have one last issue that I forgot to include in the initial post. Since my input dataset is very large (6383 sub-bricks), I'm getting the following memory error:
++ total shared memory needed = 16,784,167,400 bytes (about 17 billion [giga])
++ current memory malloc-ated = 4,223,042 bytes (about 4.2 million [mega])
** FATAL ERROR: Can't create shared mmap() segment
** Unix message: Cannot allocate memory

I'm running this on my university's HPC, where I requested 20gb of virtual memory, but the error still persists.

Thanks again,

Dan
Subject Author Posted

3dDeconvolve: Trouble Diagnosing Warning Messages

Dan October 04, 2018 04:54PM

Re: 3dDeconvolve: Trouble Diagnosing Warning Messages

rick reynolds October 04, 2018 06:38PM

Re: 3dDeconvolve: Trouble Diagnosing Warning Messages

Dan October 04, 2018 09:16PM

Re: 3dDeconvolve: Trouble Diagnosing Warning Messages

rick reynolds October 04, 2018 10:15PM

Re: 3dDeconvolve: Trouble Diagnosing Warning Messages

Dan October 04, 2018 10:42PM

Re: 3dDeconvolve: Trouble Diagnosing Warning Messages

rick reynolds October 04, 2018 11:35PM

Re: 3dDeconvolve: Trouble Diagnosing Warning Messages

Dan October 05, 2018 09:34AM

Re: 3dDeconvolve: Trouble Diagnosing Warning Messages

rick reynolds October 05, 2018 09:42AM