Show all posts by user
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
Page 1 of 2
Pages: 12
Results 1 - 30 of 33
The 13-16 brain images represent biological replicates taken at two time points. Every individual was sampled once. The resolution is approximately 7um on a side per voxel. The average values across the six groups from (3dFWHMx -2difMAD -demed) are x11.54241667, y10.11580833, z13.35278333.
Based on your comment, it sounds like -detrend was inappropriate given this design, correct?
by
Matt_McNeill
-
AFNI Message Board
Thanks very much for your suggestions.
To test your suggestion, I created six concatenated files of unique brain images (n=13-16 brains each). I calculated agreement of FWHMx smoothness estimates across the six files by taking the stdev / mean. I found that for my sets, I had the best agreement amongst the group when using the combination of (-2difMAD -detrend 2). I had lesser agreement for ot
by
Matt_McNeill
-
AFNI Message Board
Does it make sense to use more than one option to remove structure from a concatenated set of PET data sets? For example, one could combine -2difMAD and -demed. Is there a way to test if this combination makes sense?
Example: 3dFWHMx -2difMAD -demed dyn+orig
by
Matt_McNeill
-
AFNI Message Board
I am trying to compare two masks using the @DiceMetric function. The masks were created with 3dCalc. However, I keep getting the following message:
$ @DiceMetric 20130925_brain202_ndufs7_resampled_10blur_testABM_3dwarped_float_masked_model.nii 20130925_brain202_ndufs7_resampled_10blur_testABM_3dwarped_float_masked_model.nii
** FATAL ERROR: Can't open dataset 'XYZ_vGnuUWiOAioBt0XU_3
by
Matt_McNeill
-
AFNI Message Board
In case it matters, I am using a newer version of AFNI to visualize the results than the version I am using the analyze the data. 3dMVM on my local machine is 2.0.0. It was downloaded and built on Sept 17 2013.
by
Matt_McNeill
-
AFNI Message Board
Hi Gang,
I am using 3dMVM version 0.2.5 from March 29, 2013. AFNIio.R was updated at the same time. All GLTs were run on the same system using the same version of 3dMVM. The rest of AFNI was downloaded and installed on 1/2/2013. 3dANOVA has this value associated with it: AFNI_2011_12_21_1014. Please let me know if you would like additional version information.
Can you tell me a little mor
by
Matt_McNeill
-
AFNI Message Board
Good morning AFNI message board,
I am running 3dMVM on the same brain images spatially normalized using two different strategies: those spatially normalized against a template brain (1) and those spatially normalized (from 1) again against a novel template brain made from an average of themselves. In the latter case, the spatial normalization is much improved, particularly for one genetic popu
by
Matt_McNeill
-
AFNI Message Board
Thanks, Gang.
I actually don't have t-statistics for each subject because each individual is measured only once. The data sets I have are more similar to a snapshot you might take of someone in an old PET study, except I really can only measure each individual once. What I would like to do is a series of pair-wise tests for variance differences between the individuals within each of the
by
Matt_McNeill
-
AFNI Message Board
What are the explanatory variables in your 3dMVM analysis in addition to two groups of subjects?
**My analysis consists of animals collected at three time points after exhibiting one of two behaviors from one of two colonies (3x2x2) for a 3-way model.
And what kind of response variable (input files from each subject) do you have?
**I have intensity information about each individual captured
by
Matt_McNeill
-
AFNI Message Board
Hi All -
After running my between-subjects GLM (3dMVM), I noticed that the variance in one group of subjects appeared to be different than that of the other group. So, I averaged the intensity values across significant regions detected in the GLM, and used an outside stats program (STATA) to look for significant differences in the variance because 1) it may be biologically relevant, and 2) I
by
Matt_McNeill
-
AFNI Message Board
Complete and ready to go. I look forward to your findings.
by
Matt_McNeill
-
AFNI Message Board
Sure, and thanks for looking at this issue.
I will send the link to your email address.
by
Matt_McNeill
-
AFNI Message Board
> By "yellow" clusters, do you mean that only the
> positive clusters show up? Do you get exactly the
> SAME positive clusters as the result from
> 3dttest++? Did you happen to turn on the button
> "Pos?" underneath the color spectrum?
Yes, only the positive clusters show up. While I haven't overlaid masks from the contrast with a mask representing t
by
Matt_McNeill
-
AFNI Message Board
Sure.
I get a total of 17 voxel clusters which pass the 3dClustSim multiple testing correction method in the main effect (experiment). When I compare the two groups represented under "experiment" using a ttest, I see that some of those groups are coming up as yellow while others of them are blue. I wanted to stay within the 3dMVM model framework, so I hoped to explore those differen
by
Matt_McNeill
-
AFNI Message Board
Thanks, Gang, for your thoughts. All variables are across subjects.
I also tried declaring "colony" with -qVars, but the results were the same. Anything else I should try?
Thanks again.
by
Matt_McNeill
-
AFNI Message Board
I'd like to add that I recently saw an oddness with my posthoc comparisons as well. I have run 3dMVM on three different data sets in at least 6 different ways. In each case, the results were confirmed by using another test (3dANOVA or 3dttest++). Recently, I ran 3dMVM on another data set with three variables and 12 posthoc contrasts. Since one of those contrasts was set to merely reveal the
by
Matt_McNeill
-
AFNI Message Board
Good morning -
I am interested in creating a graph of the voxel intensity levels across time in order to describe the pattern of voxel intensity change over time. I have a series of files which each has only one time brik associated with it. Using software designed microarray data analysis, I can find temporal patterns, but I need to export the intensity of each voxel within a mask into a .1D
by
Matt_McNeill
-
AFNI Message Board
I am interested in looking at voxel intensities across groups using only a single time point per *.nii file. Is there program available that can do that?
by
Matt_McNeill
-
AFNI Message Board
One more question regarding 3dMVM. All of my starting files are in the +orig space, but my first successful output of 3dMVM is +tlrc. Can I change the output to be +orig like my starting files?
Thanks,
Matt
by
Matt_McNeill
-
AFNI Message Board
Hi All -
I have used 3dttest++, 3dANOVAx, and GroupAna. I am now learning to use the new 3dMVM for the first time, and I am running it on a cluster. I hope you can help me answer two questions.
1) When I submit a 3dMVM job to the cluster by first specifying that I want the cluster to allocate 4 cores to my job (PBS, qsub) "nodes=1:ppn=4" and I use the 3dMVM option -jobs 4, I get
by
Matt_McNeill
-
AFNI Message Board
I appologize if I am posting this twice, but I am concerned that because I turned my computer off while working on the post yesterday (then submitting yesterday) it didn't go through.
My goal is to use 3dClustSim on data sets that have a lot of anatomical information left in them. Overall, I am interested in looking at the regions containing cell bodies. This allows me to mask out everyt
by
Matt_McNeill
-
AFNI Message Board
Hi -
I have run 3dANOVA and GroupAna on two different sample sets, and I am now looking at the data. In each case, there are two sub-bricks per level. I believe that the second sub-brick is the F-statistic (since it generates p-value output in AFNI GUI), but the first sub-brick I'm not sure about. I can find information about what that one represents for 3dttest++ and 3dttest, but I'
by
Matt_McNeill
-
AFNI Message Board
Page 1 of 2
Pages: 12