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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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Hi again, Gang,
Thank you for your previous help! I have a couple of follow up questions for you. I am performing the analyses we discussed above for the moderation using 3dttest++ and looking at option to do multiple comparisons correction using ClustSim and ETAC. The current documentation states that ETAC correction is not accurate for covariates. Is this still the case? Can the ETAC maps o
by
sewilliams
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AFNI Message Board
Hi Gang,
After reading the documentation for both commands I want to make sure I'm accurately conceptualizing how I would run these analyses. If you could let me know whether my thought process about this is accurate that would be great.
With 3dttest++, for example, would essentially run a t-test to compare the younger and older adult groups to one another by putting the YAs into set
by
sewilliams
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AFNI Message Board
Hi all,
I am working on some functional analyses for which I have correlated voxel-based whole-brain activation with our behavior of interest across all participants using 3dTcorr1D. We would like to test for voxel-based group differences between younger and older adults on the relationship between our behavioral measure and brain activation (i.e., test for a significant group moderation effe
by
sewilliams
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AFNI Message Board
Hi all,
I am working on using @toMNI_Qwarpar to create a nonlinearly warped atlas for my dataset. I have run @toMNI_Awarp successfully on each individual dataset, and am trying to run @toMNI_Qwarpar in the directory created by @toMNI_Awarp.
However, when I run @toMNI_Qwarpar I receive this fatal error message and the script eventually dies:
$ ./OASES_qwarp.sh
========== @toMNI_Qwa
by
sewilliams
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AFNI Message Board
Hi again,
I was able to get the script to run through to the end without stalling, but I am receiving a lot of errors during the @auto_tlrc process, so I am unsure if the received outputs are correct.
I looked through the @auto_tlrc documentation but I'm not sure what the problem might be. Would you be able to look at some of these messages and help me identify if they are an issue? P
by
sewilliams
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AFNI Message Board
Hi again,
I am still having some trouble running this script on the server where my data is located. Once I copied the template into my local directory, the script starts running but then stalls during the 3dUnifize loop.
I am running this code as a test, and I receive the folllowing output:
williamss@linux5% @toMNI_Awarp awarp 401_MPRAGE_strip+orig.HEAD 402_MPRAGE_strip+orig.HEAD
mkd
by
sewilliams
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AFNI Message Board
Thanks so much Daniel! I should have thought of copying the dataset to my local directory - it seems to be running now.
Thanks again,
Sam
by
sewilliams
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AFNI Message Board
Hi all,
I am trying to run @toMNI_Awarp on my skullstripped MPRAGE files using this line of code:
@toMNI_Awarp awarp_test 401_MPRAGE_strip+orig.BRIK 402_MPRAGE_strip+orig.BRIK
and receive the following error:
***** @toMNI_Awarp: Failed to find template MNI152_1mm_uni+tlrc -- cannot continue
However, I can locate this file within my AFNI version - is there some way to point the
by
sewilliams
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AFNI Message Board
Hi Bob,
Thanks for the input. While we are not doing any segmentation, we are prepping our images to create a template using @toMNI_Awarp and @toMNI_Qwarpar. The template will be used to compare younger and older adult samples. Do you think the small brightness patches will matter in that case?
Also, I noticed after my last message that the 3dunifized images show this bright rimming/halo
by
sewilliams
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AFNI Message Board
Hi all,
I am working on prepping images for preprocessing and running my MPRAGE files through 3dUnifize prior to using 3dSkullStrip.
I can definitely see that intensities have been normalized after 3dUnifize, but I am concerned about some peripheral areas of the white matter that still appear brighter than the rest, specifically areas close to the cortex. I tried adding the -gm option an
by
sewilliams
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AFNI Message Board
Hi Dan,
Thanks for the response. Could you clarify further why we would need to create two separate templates? If we normalize each groups to a different template we would not be able to compare them, correct? And comparing young vs old is the primary goal of the study. Our goal end product is to have one atlas that merges young and old subjects. Do we create a young and old template, and th
by
sewilliams
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AFNI Message Board
Hi all,
I am working on an fMRI study comparing older adults to young adults. We are running our analyses in AFNI and would like to make one atlas from our subject data that could be utilized for preprocessing all participants. This technique was suggested during my lab's attendance of the AFNI Bootcamp at WashU in January.
I have gathered some resources from the workshop (specifica
by
sewilliams
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AFNI Message Board