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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
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Dear Gang,
I have ran the GLT codes at you have suggested them, i.e.:
-gltLabel 1 interaction -gltCode 1 'Group : 1*treatment_1 -1*treatment_2 Time : 1*pretreatment -1*posttreatment' \
-gltLabel 2 interaction_t1 -gltCode 2 'Group : 1*treatment_1 Time : 1*pretreatment -1*posttreatment' \
-gltLabel 3 interaction_t2 -gltCode 3 'Group : 1*treatment_2 Time : 1*pretreat
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Matthew_2
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AFNI Message Board
Dear Gang,
Thank you for your help, I will move forward with one of 3dMVM or 3dANOVA3 (type 5).
Also I have a related question, I am particularly interested in testing what is sometimes called a "spreading interaction". That is, I'd like to specifically test for an interaction that captures a difference in posttreatment resting-state functional connectivity (rsfc) between gro
by
Matthew_2
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AFNI Message Board
Dear Gang,
Thank you for your quick response! Here are answers to your questions:
1) Any missing data?
No missing data
2) Equal number of subjects across the two groups?
The groups are unequal in size, something like 18 and 14
3) Do you have t-statistic available for each effect estimate (beta)?
I was planning to run the model on z-score maps that were converted from pearson corre
by
Matthew_2
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AFNI Message Board
Dear AFNI experts,
My goal is to create whole-brain statistical maps for the interaction of brain data between two groups of individuals who received a different treatment and were scanned pre- and post-treatment. I'd like to see how the brain changed differentially between treatments.
I am not an expert in this aspect of AFNI and I see that there appear to be many options to do this,
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Matthew_2
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AFNI Message Board
Hi Gang,
Thank you, this makes sense.
I have a followup question, is there a way to code using 3dMVM a "slope" across three contrasts. For example, if I have two groups and three conditions (A, B, C), is there a way to test whether the "slope" between the two groups differ at any given voxel. Basically the slope would be a relationship computed between betas from A, B, a
by
Matthew_2
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AFNI Message Board
Hi Gang,
Thanks for your help.
After I have included the two GLTs that you have recommended, then I used 3dcalc for conjunction analysis a described here on one of your webpages:
I then have a 3d volume with values 0, 1, 2, and 3. The 3s are what I am interested in, of course, as a 3 represents voxels in which both statistical tests reached the significance value defined using 3dcalc.
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Matthew_2
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AFNI Message Board
Dear AFNI experts,
I think this question is best directed at Gang, as it concerns whole-brain interaction modeling using 3dMVM.
I have data from two groups (healthy and diseased), and they each completed three tasks during fMRI acquisition (task_1, task_2, task_3). I am interested in testing for a group interaction on the linear contrast that beta values are greatest for task_1, then task_
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Matthew_2
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AFNI Message Board
Hi Gang,
Thank you for your message, very interesting and helpful.
Regarding modeling our data using 3dMVM with a covariate: our groups have a difference in age (t-test p = 0.0457; M/SD/min/max, GRP1 = 30.2/11.2/18.9/52.1, GRP2 = 38.1/9.4/22.8/51.1). Based on your webpage on covariates and centering it seems that best would have been to recruit groups that did not differ by age. Since I can
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Matthew_2
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AFNI Message Board
Hi AFNI experts,
I write with a question regarding using 3dFWHMx to assess smoothness of data processed in FSL. I intend to use 3dClustSim with the average group-level smoothness information.
Typically when I use 3dFWHMx I run it on the preprocessed (including motion correct, registered/warped to a template) time-series data with the -detrend option, or without the detrend option on GLM res
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Matthew_2
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AFNI Message Board
Dear Gang and the AFNI experts,
This question concerns usage of 3dMVM, so I assume that it should be directed at Gang.
I'm interested in running ANCOVA, with 1 between-subjects factor (group, two levels) and 1 within-subjects factor (condition, three levels), and age as a covariate. I am interested in the group x condition interaction. I have two questions about this.
1. I am includ
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Matthew_2
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AFNI Message Board
Dear AFNI gurus,
I'm writing about using the AFNI matlab tool WriteBrik.m
My intention is to run statistics in matlab and then write a brik that can be used in AFNI's viewer GUI with cluster thresholds defined from 3dClustSim.
I've ran statistics on a voxel-wise basis using matlab, resulting in a p-value for each voxel for a particular masked region. I've used BrikLoa
by
Matthew_2
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AFNI Message Board
Dear AFNI experts,
I am interested in getting single coordinates from a template (e.g., MNI) space into individual subject space in approximately the same spatial/anatomical location.
This process will need to take about 20 mins or less.
My idea is to compute a non-linear warp from individual space to the template, and then use the inverse warp from this to convert single coordinates in
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Matthew_2
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AFNI Message Board
Hi AFNI gurus,
I have a question about dilating ROIs/masks.
I'm interested in dilating an roi by a particular *mm* value. 5 mm in particular. Of course functional or other voxels may be not a perfect size for this, but then I imagine some kind of rounding will occur.
I've seen a post here:
But the links are broken.
I see that 3dcalc, and 3dautomask, and 3dmasktool have opt
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Matthew_2
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AFNI Message Board
Hi Peter,
Thank you for your help with this.
I'm not resampling functional images to an anatomical template with 1^3 mm voxels. I'm using a lightly customized afni_restproc.py with a custom template for the @auto_talairach step. The template originally had 256^3, 1^3 mm voxels, with a lot of zero-padding. Perhaps only half of the center voxels of any given dimension have brain dat
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Matthew_2
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AFNI Message Board
Hi Peter,
Thanks for the clarification.
I've applied 3dAutoBox to the template that I'm using, so all individuals will be warped to the same cropped space. It's a non-standard MNI brain that has been conformed and interpolated from FreeSurfer.
I've tested various things (like origin, template space markers, voxel size) in the 3dAutoBox-ed image, and they are all as th
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Matthew_2
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AFNI Message Board
Thank you Peter, this is helpful.
If possible, could you be a little bit more explicit about what "headaches" you anticipate? Do you mean something like volumes that won't align if I've cropped some and not others?
I'd hope that 3dAutobox doesn't change anything regarding the origin, space, voxel sizes or transforms or anything like that... I'll do some ch
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Matthew_2
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AFNI Message Board
Dear AFNI gurus,
I have an image that is 256 x 256 x 256 with voxel size of 1 mm, many of these are zero-valued voxels. I intend to crop the image so as to improve processing speed. Is this recommended? If so, what tool can do this? I've looked over 3dresample, 3drefit, and others and have not seen the capability that I am looking for. I see that many of AFNI's programs do not proces
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Matthew_2
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AFNI Message Board