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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
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Just wanted to update everyone.
Crazy thing, I ran this locally on my windows laptop:
Dell Latitude 5500
Processor Intel(R) Core(TM) i5-8365U CPU @ 1.60GHz 1.90 GHz
Installed RAM 32.0 GB (31.8 GB usable)
System type 64-bit operating system, x64-based processor
WSL Ubuntu 18.04.3 LTS
4.4.0-19041-Microsoft
And it worked just fine.
by
tpderamus
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AFNI Message Board
So sorry forgot to mention.
Have since upgraded to:
afni -ver
Precompiled binary linux_ubuntu_16_64: Jun 6 2022 (Version AFNI_22.1.13 'Antoninus Pius')
And moved from Ubuntu to Pop:
lsb_release -a
No LSB modules are available.
Distributor ID: Pop
Description: Pop!_OS 22.04 LTS
Release: 22.04
Codename: jammy
On this machine.
by
tpderamus
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AFNI Message Board
Well hate to say it but I need to re-run this particular analysis and the problem is occurring once again.
I've tried the swapspace fix that I ran previously, but unfortunately it is no longer working even if I pump the swapspace all the way up to 20G and run it with 8 of my 12 cores.
Theoretically the data is much smaller here, since I'm using the single-band reference image as o
by
tpderamus
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AFNI Message Board
So this is the singularity I pulled, I did not use the Neurodocker:
singularity pull docker://afni/afni_cmake_build
singularity run afni_cmake_build_latest.sif
Precompiled binary 1: Mar 4 2021 (Version AFNI_99.99.99 'Alexios V Doukas the Bushy-eyebrowed')
by
tpderamus
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AFNI Message Board
Hey just wanted to add this as a follow up.
The computer I initially ran this on was an Ubuntu box with 32G of memory so I was really surprised when it threw that error.
However, it came to my attention that the swap-space likely wasn't very big on the default settings.
As such, I did the following to increase the swap-space memory (requires sudo permissions):
sudo swapoff -a
su
by
tpderamus
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AFNI Message Board
Hi AFNI base.
I'd like to use 3dICC and 3dLMEr on our high performance computing cluster without having to create a new AFNI module, and I figured using the AFNI singularity container would be a good way to do this.
I've run the following:
```
singularity pull docker://afni/afni_cmake_build
singularity run -B /data/$USER/workdir:/home/afni_user/work --cleanenv afni_cmake_buil
by
tpderamus
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AFNI Message Board
Hi All.
I'm having some issues with 3dICC.
I'm attempting to run it to find voxel-wise ICC values across 30 preprocessing pipelines (using the mean images from each due to storage space constraints).
However, while the code itself seems to work, it dies just prior to running, only giving me a "Killed" notification in the window.
Am I doing something wrong on the in
by
tpderamus
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AFNI Message Board
Tried to attached it but the forum wouldn't accept anything that wasn't an image.
The delimiter is a tab, should it be something else?
by
tpderamus
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AFNI Message Board
That call resulted in the following:
3dICC -prefix Warp_ICC3 -jobs 1 \
> -mask 'MaskofMasks.nii' \
> -model "1+initializer+target+(1|Subj)" \
> -dataTable @Inputfiles.txt
Read 13000 items
Error in if (len%%wd != 0) errex.AFNI(paste("The content under -dataTable is not rectangular !", :
argument is of length zero
Calls: process.ICC.opts
Executio
by
tpderamus
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AFNI Message Board
Hi all.
Wanting to run 3dICC to check for differences in the average signal across 19 different pre-processing strategies and I'm running into some issues with string parsing.
I'm running it on my local machine with the following:
3dICC -prefix Warp_ICC3 -jobs 1 \
-mask 'MaskofMasks.nii' \
-model "1+initializer+target+(1|Subj)" \
-InputFile 'inputfil
by
tpderamus
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AFNI Message Board