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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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Nevermind, I figured it out
-bsVars 'BPRS+age+sex+FD' \
-qVars 'age,FD' \
The variables between-subject since I'm only analyzing one data point per subject, not multiple ones. I get confused by the terminology.
Thanks!
by
Omar Maximo
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AFNI Message Board
Yes, these variables were acquired for all subjects at baseline, except for BPRS. BPRS variable is the percent change score from baseline and after 16 weeks of treatment.
Maybe 'sex' could be consider a between-subjects factor
by
Omar Maximo
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AFNI Message Board
3dMVM - 2 years ago
Hi AFNI gurus,
Im trying to run a regression looking at change in some clinical score (BPRS) with baseline functional connectivity using 3dMVM with some covariates. I'm only looking at one group only (not doing 2-group comparisons). Here's my script
3dMVM -prefix pathtoprefix/results_3MVM_ECN_baseline.nii -jobs 12 \
-mask pathtomask/ECN_mask.nii \
-bsVars 1 \
-wsVars 'BPRS
by
Omar Maximo
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AFNI Message Board
-gltCode 1 'Session: 1*S1 Group : 1*HC -1*FEP'
-gltCode 2 'Session: 2*S2 Group : 1*HC -1*FEP'
-gltCode 3 'Session: 3*S3 Group : 1*HC -1*FEP'
So, this is how it would look for all 3 comparisons then?
Thanks a lot!
by
Omar Maximo
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AFNI Message Board
Hi again,
I want to compare each group at each time point. Is this how my glts should look like?
-num_glt 3
-gltLabel 1 'HC-FEP_ses-01' -gltCode 1 'Session: 1 : 1*HC -1*FEP' \
-gltLabel 2 'HC-FEP_ses-02' -gltCode 2 'Session 2 : 1*HC -1*FEP' \
-gltLabel 3 'HC-FEP_ses-03' -gltCode 3 'Session 3 : 1*HC -1*FEP' \
by
Omar Maximo
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AFNI Message Board
Hi AFNI,
I'm trying to run a linear mixed model using 3dLME between 2 groups across 3 different sessions/time points (some subjects have missing data) while controlling for age, sex, and framewise displacement. I just want to make sure my script looks ok. I'm trying to model a group x session interaction while controlling for the aforementioned variables. With ~1+RT, Im specifying di
by
Omar Maximo
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AFNI Message Board
Gang Wrote:
-------------------------------------------------------
> Omar,
>
> I'm confused with your description. Are you
> talking about voxel-wise time series for each
> subject? Is this a subject- or population-level
> analysis? With the former, how do gender and age
> come into play? With the latter, you would have to
> elaborate it more. What is exact
by
Omar Maximo
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AFNI Message Board
Hi,
I have the following question.
I have data from CONN (denoised whole brain time series) and would like to account for age and gender, and I used 3dttest, but it only takes 3d images.
I figured you can use -brickwise and -covariates at the same time, but -resid cannot be used with brickwise. Is there another option to do this: account for age and gender on a time series.
Best,
Oma
by
Omar Maximo
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AFNI Message Board
Peter Molfese Wrote:
-------------------------------------------------------
> Please post all the commands you've run written
> out.
I ran auto_warp.py -base IITmean_FA.nii -input sub-control01.ses-01.FA.warped_5mm.resample.rotate.flipped.nii.gz -skull_strip_input no and it seemed like it worked.
by
Omar Maximo
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AFNI Message Board
- We'll need some more information. Is the FA map in subject space? Standard space? Is it our version of the atlas or someone else's?
I ran 3dinfo on them and it says orig, but these images were warped to the IIT template (https://www.nitrc.org/projects/iit/). What I did was run 3drefit -space MNI so I could work with them.
The ROIs come from that same IIT link above.
Let me
by
Omar Maximo
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AFNI Message Board
Hi Afni gurus,
I am trying to align an ROI from the IIT atlas V5 to FA maps. Both images were normalized to the IIT_mean_FA map.
I tried 3dresampling the ROI to the FAP maps, but they end up looking like this.
Any suggestions.
Best,
O
by
Omar Maximo
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AFNI Message Board
3dReHo - 11 years ago
Hi,
In 3dReHo, -neigh_RAD R, Is R defined in millimiters or what is the unit of measurement? Let's say that I wanted to look at a radius of 14mm, would I need to type -neigh_RAD 14, or what would the equivalent be for such measure? A spherical seed with radius of 14mm is approximately 400 voxels (using 3x3x3mm isotropic voxels), but when I typed 14 in the -neigh_RAD option, it said that i
by
Omar Maximo
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AFNI Message Board
I would like to calculate KCC using a larger neighborhood on every voxel. The idea for this is to compare it to a similiar method that looks at local connectivity using graph theory. In this paper, Sepulcre et al., (2010) used a radius of 14mm to assess neighboring voxels that had a similar time series correlation to the reference voxel, only excluding those with r < .25. I calculated that usi
by
Omar Maximo
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AFNI Message Board
Hi,
Is there a way that 3dreho can be manipulated so we could calculate KCC using larger cluster sizes > 27 voxels?
Where in the C code would we need to make the changes and would these changes change the code significantly?
Thanks,
Omar Maximo
by
Omar Maximo
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AFNI Message Board