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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:
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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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Hello,
Sorry if this is a duplicate. I tried posting but I don't see it. Anyway, I just wanted to solve one additional problem. I am interested in the Age main effect, specifically the direction of it. The F test is reported, but it doesn't provide the slope.
I assume I can run the following?
'DxGroup : 1*ADHD -1*Typical Age : '
'DxGroup : 1*ADHD Age : '
by
anthonystevendick
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AFNI Message Board
Hello!
Long time listener...
I'm using 3dMVM. Here I am interested in the age by diagnostic group interaction as it predicts the brain outcome measure. I am getting the following error:
Error in `[.data.frame`(lop$dataStr, , jj) : undefined columns selected
Calls: process.MVM.opts -> [ -> [.data.frame
Execution halted
Here is the (truncated) command. Do I need the -glt o
by
anthonystevendick
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AFNI Message Board
Thanks Gang. A suggested future addition, to make this more straightforward, is to have a 3dLM version of 3dLMEr (or even better, allow robust linear modeling as well). But that may be down the line. In the meantime, a quick question about 2).
For 2) Remove the population mean of 'brain' at the voxel level and call it BRAIN;
Is that a 3dcalc command in which mean is the mean of a
by
anthonystevendick
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AFNI Message Board
Yes, brain is a 3d volume with beta weights from 3dDeconvolve for each subject.
So by voxel,
y = PTSD measure (continuous)
x = Exposure measure (continuous)
n=300
lm(formula = PTSD ~ Exposure*%signal change beta + age + sex + race_ethnicity + education + marriage status + income + device, data = dat)
Can 3dRegAna do interactions of this type? Or maybe 3dMEMA?
Anthony
by
anthonystevendick
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AFNI Message Board
Hello!
I'd like to run the following regression model on a voxel-wise basis. I specified it in R syntax because I basically want something like 3dLMEr, but without the mixed-effects.
I thought 3dRegAna would do this, and maybe it does, but it doesn't appear that I can model the interaction of a behavioral and brain variable. Thanks for any help!
The model:
lm(formula = y ~ x
by
anthonystevendick
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AFNI Message Board
Hello Paul,
I got everything to work and now I understand the pipeline a little better. I am putting the code up on Github and will send the link when it is up. Basically the Lausanne is the freesurfer parcellation, further parcelled into finer bits. So IMO it is a better parcellation because enormous ROIs like superior frontal gyrus are more fine-grained. And of course you can always combine
by
anthonystevendick
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AFNI Message Board
I can report some success with v2.2.1. The REN files for aparc and a2009 populate fine. However, it does not appear to grab the lausanne flag to make the new lausanne atlas REN files. The lausanne atlas is a further parcellation of a2009.
The command I run is:
e.g., @SUMA_Make_Spec_FS -extra_annot_labels lausanne2008_aparc -NIFTI -fs_setup -sid 1130911
In the past, I edited the origin
by
anthonystevendick
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AFNI Message Board
Okay, so I have updated my script to add one atlas, and also run AlignToExperiment as part of @SUMA.
@SUMA_Make_Spec_FS -extra_annot_labels lausanne2008 -NIFTI -sid $sub
This should give me what I want (an a2009 atlas, and a lausanne atlas which was created earlier, aligned to the original T1 that went into freesurfer). Am I on the right track here?
by
anthonystevendick
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AFNI Message Board
Ah, this very helpful. Our AFNI install is old at this point, so I think that is the first thing to update that. I lose region information during the resampling steps. My goal is to end up with a matrix subjects by region, so any suggestions that get to that are super helpful.
Here is my bash script, simplified:
#!/bin/bash
module load afni/17.3.06
cd <path>/noddi/dset/derivatives
by
anthonystevendick
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AFNI Message Board
Somebody must have a solution for this, but I can't find one.
In a loop, I run:
3dROIstats -numROI 194 -zerofill NA -mask <path>/freesurfer_v6/$s/surf/SUMA/aparc.a2009s+aseg_rank_Alnd_Exp_noddi_frac+orig \
<path>/noddi/dset/derivatives/sub-"$s"/ses-S1/NODDI/NDI.nii.gz > <path>/noddi/dset/derivatives/sub-"$s"/ses-S1/NODDI/NDI_a2009.txt
T
by
anthonystevendick
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AFNI Message Board
Is there a reason you're staying in the surface? Are you okay with using the parcellation in the volume space (which will allow you to look at subcortical structures)?
by
anthonystevendick
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AFNI Message Board