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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
History of AFNI updates
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afni -ver
Precompiled binary linux_openmp_64: Feb 19 2015 (Version AFNI_2011_12_21_1014)
afni_proc.py -ver
version 4.30, February 13, 2015
Would this version not have the current options?
by
krasmussn
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AFNI Message Board
** error: option -dsets follows unknown arg #11 (-anat_follower_ROI)
I thought this was odd so looked in the afni_proc.py -help output. There is nothing there to indicate -anat_follower_ROI is a valid option (I had been previously using example 11 as a template, but that seems to be gone as well.
by
krasmussn
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AFNI Message Board
Hello!
A few months ago I had been using afni_proc.py successfully with the following options (see below). I tried running new subjects through this script this week and have noticed that -anat_follower_ROI is no longer a viable option. Do you have any suggestions for what to use instead to ensure consistency with the outputs of previous scans processed with this script?:
afni_proc.py -s
by
krasmussn
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AFNI Message Board
I believe deleting the large afni command log was the trigger.
by
krasmussn
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AFNI Message Board
Thank you - it seems to be working now. I appreciate the help!
by
krasmussn
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AFNI Message Board
Good morning,
I have been having afni crash on me at various stages of viewing and attempting to save images since late yesterday evening. I have attached the terminal output and crash log from the most recent failure below. Any ideas you have on getting this fixed would be much appreciated.
Thanks!
Kate
Precompiled binary linux_xorg7_64: Jan 27 2016 (Version AFNI_16.0.01)
Thanks go t
by
krasmussn
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AFNI Message Board
Yes, it would be ideal if we could only remove the local white matter signal.
Here is the current command:
afni_proc.py -subj_id ${SUBJID[$n]}_${MRQID[$n]} \
-out_dir $restdir/${SUBJID[$n]}/${MRQID[$n]}/output \
-script $restdir/${SUBJID[$n]}/${MRQID[$n]}/proc_script.sh \
-blocks regress \
-copy_anat $fsdir/mri/aseg+orig \
-anat_follower_ROI aaseg anat $fsdir/SUMA/aparc.a2009s+ase
by
krasmussn
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AFNI Message Board
Thanks for your help, Rick!
Could you help us understand what's happening at Deconvolve versus the following steps (below) when dealing with local white matter? Is 3dDeconvolve first taking out a global white matter signal then dealing with local white matter in a second step? And if so, why would we want the white matter regressed that way? Is there a way regress local white matter only?
by
krasmussn
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AFNI Message Board
Thanks Rick. Since I adjusted for the -regress_anaticor, I added the mask block (because the script wouldn't run otherwise). The above error is still occurring even after I add that block.
by
krasmussn
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AFNI Message Board
Thanks Rick, adding -regress_anaticor did work to get the WM regression going, however now I am running into another problem. When I use either -regress_anaticor or -regress_anaticor_fast the script exits before completion with this error:
3dTcat -prefix all_runs.IRK9294_63047215 pb00.IRK9294_63047215.r01.tcat+orig.HEAD
++ 3dTcat: AFNI version=AFNI_16.0.00 (Jan 1 2016) [64-bit]
3dTcat -pr
by
krasmussn
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AFNI Message Board
We ran afni_proc.py intending to regress out local white matter using the option -regress_anaticor_radius, however in looking at the output script, there is no evidence that the white matter regression was run. We have done this with 10mm, 15mm, and 20mm radii but with no luck. Is there something we should be doing differently here?
This is the script we are using:
afni_proc.py -subj_id $
by
krasmussn
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AFNI Message Board
Hi Rick,
I just want to confirm with you that afni_proc.py does NOT use DVARS and FD for motion correction as does afni_restproc.py. That seems to be the case based on the -help output, but we were not sure.
Thanks! Kate
by
krasmussn
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AFNI Message Board
We have run afni_restproc.py successfully, but now we are trying it with the FD and DVARS options. We are getting an error saying that we have to have the -align option on. However, in the past we have kept it off because we are handing it preprocessed data. With align on, it runs 3dvolreg then tries to do a SkullStrip on the functional image using 3dSkullStrip. It appears to fail when using 3dS
by
krasmussn
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AFNI Message Board