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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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Hello - I am trying to use 3dLMEr to run a trial-wise LME analysis (N=90 x 60 trials extracted using IM model)
Whenever I try to do this I get a memory error while reading in the images.
"Error: vector memory exhausted (limit reached?)"
Any suggestions? Or way to tell how much might be needed?
by
dpagliaccio
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AFNI Message Board
Hi
I have it set up with 24 ROIs and 54 participants
Basically 50/50 split for diagnosis and sex
Age and IQ are z-scored continuous variables
by
dpagliaccio
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AFNI Message Board
Hi
I am trying to run an RBA across 24 ROIs but am getting an error: The model does not contain posterior samples.
I have updated my brms package in R and tried a simplified model with just an intercept, but no luck
Command here:
RBA -prefix outrba \
-Subj subject -ROI region -Y Y \
-chains 1 -iterations 1000 \
-model '1+Dx+Sex+ageZ+IQZ' \
-cVars 'Sex,Dx' -qVars &
by
dpagliaccio
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AFNI Message Board
Hi Gang,
I know this is an old thread now, but just wondering if there were updates on this front.
Particularly, I am have a dataset where I have 3dAutomask-ed each individual's image to remove dropout regions. I was hoping to have this excluded person/voxel-wise in the group-level 3dLME - but it seems like it may be reading this in as zero values. I tried using the -bounds options but am
by
dpagliaccio
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AFNI Message Board
Two postdoctoral positions are available within the Translational Research on Affective Disorders and Suicide Laboratory at Columbia University (auerbachlab.com). Fellows will be co-mentored by Dr. Randy P. Auerbach and Dr. David Pagliaccio. The postdoctoral fellows will support NIH/NIMH and foundation-funded projects that aim to identify neural (structural and functional MRI) and real-time (e.g.
by
dpagliaccio
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AFNI Message Board
I am trying to run afni_proc on HCP pipeline output in CIFTI space - specifically creating parcellated timeseries for a particular atlas and converting to a 'fake' nifti format using workbench tools. The resulting input files to afni_proc are #ofROIs x 1 x 1 size .nii files. When afni_proc copies the data in the first step to create pb00 files, 3dTcat is automatically turning this into
by
dpagliaccio
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AFNI Message Board
The deadline for this position has been extended. please email Rachel.Marsh@nyspi.columbia.edu or David.Pagliaccio@nyspi.colum&
by
dpagliaccio
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AFNI Message Board
I was just wondering if there was a way to apply a notch filter to motion regressors - either with a 1D function or ideally as part of afni_proc?
Per recent suggestions: ,
by
dpagliaccio
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AFNI Message Board
Employer: Columbia University College of Physicians & Surgeons, Division of Child and Adolescent Psychiatry
Location: New York, NY, USA
Positions available: July 1, 2020
A slot in a NIMH funded postdoctoral training fellowship in child psychiatry research (2 to 3 years) is available to a child psychiatrist, psychiatrist, neuroscientist, or psychologist to conduct MRI research in chil
by
dpagliaccio
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AFNI Message Board
Hi
I am setting up first-level GLMs for a task where error-related activity is one key contrast of interest. I am wondering if there is a way to handle imbalances in the number of trials between conditions in a contrast, i.e. error vs. correct trials, if a participant only makes errors on 10-20% of trials, for example. Would this negatively impact the estimation of the contrast if they are not w
by
dpagliaccio
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AFNI Message Board
Hello,
I am running a two group analysis with 3dMEMA (including the -unequal_variance -HKtest -model_outliers -residual_Z flags).
There are some subjects that seem like outliers in the dataset but I was unclear how best to use the output of 3dMEMA to identify them. Would you be able to help clarify if there are appropriate thresholds to examine output images for issues?
-For the main outp
by
dpagliaccio
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AFNI Message Board