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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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Pages: 12
Results 1 - 30 of 47
Hi Gang,
I did what you said and I'm fully convinced now.
I just have one question left: when we report this method in our paper, can we say it's single-subject repeated measure ANOVA? Is there any paper you know that used this method before and I could read it as an example?
I would also be happy to read through the math behind this contrast to understand how it calculates th
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swallowwly
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AFNI Message Board
Hi Gang,
This is very interesting and not quite intuitive to me.
Following your explanation, let's say if I have increasing values from a1 to a9. Each neighboring step is quite small but the difference between a1 and a9 is big. And in a 'neighboring' contrast like 'a1-a2 \ a2-a3 \ a3-a4 \...', I would expect that none of these pairs would be significant, but you th
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swallowwly
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AFNI Message Board
Hi AFNI team,
For a single subject, the stats file would have voxel-wise betas, t-stat and F-stat for each regressor (in my case, an experiment condition). With this information, how do I calculate a beta's upper and lower bound of 95% confidence interval?
Thank you!
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swallowwly
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AFNI Message Board
Hi Gang,
This contrast seems to test any 'neighboring' contrast has a significant difference. If I want to test between any conditions, should I define Combination(9,2)=36 pairs that include all possible 'two-condition' pairs?
Or are you saying these 8 neighboring pair is equivalent to the 36 pairs?
Plus, I'm actually not totally sure if the 36 pairs contrast, w
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swallowwly
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AFNI Message Board
Hi Afni team,
My experiment has 9 different conditions, let's say it's a1, a2, ... a9. I want to find the voxels that shows any significant difference between any conditions. Basically, it's a one-way anova.
The problem is that I want to do this within each subject, not across subjects. I think I should do this with 3dDeconvolve, but how should I define the contrast?
Than
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swallowwly
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AFNI Message Board
Hi AFNI team,
I'm using 3dFDR to threshold my stats files for the first time, and I would like to confirm with you that I'm using it correctly. I don't understand something happened in the results...
I used 3dDeconvolve with -xsave option to calculate a new contrast. This contrast is something like +condition1 \+condition2 +\condition3 .... So in the end, I care about the F s
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swallowwly
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AFNI Message Board
Yes, thank you!
I think I meant to type the correct way but made a mistake. Thanks for correcting it!
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swallowwly
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AFNI Message Board
Hi Gang,
Thanks for the reply. Let me make sure with you about the interaction, and let's forget about the frequency just for simplicity:
my script was:
a1b1-a1b2-a2b1+a2b2
My understanding is: this is (a1b1-a1b2)-(a2b1-a2b2), it will contrast (b1-b2)'s differences in a1 and a2 condition, so that if there is any interaction effect, it will show.
Your suggestion was:
a1b1-a
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swallowwly
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AFNI Message Board
Hi Rick,
Thank you for your helpful advice! I'll definitely try to use the options to speed up this process.
Just one more question: if I directly ran 3dDeconvolve without running afni_proc.py, what's the way as equivalent to -regress_compute_fitts? Is it simply deleting the -fitts option?
Thank you!
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swallowwly
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AFNI Message Board
FYI, the input pb04* for the 3dDeconvolve step is ~32GB. It has 32 runs, each has a size of around 1GB.
I used the -mask option so the analysis should be performed within the brain. I'm considering using 3dZcutup to allow me to run them in smaller RAM computers...
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swallowwly
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AFNI Message Board
Hi Rick,
Thanks for the quick reply!
If I'm using afni_proc.py, it failed at the regress step. Sometimes it looks something like
voxel loop: 012
killed
If I'm using 3dDeconvolve, it's the same situation.
The input to this step is usually around 32GB combining all the pb04* files. And the computers I'm running on are all iMac computers with MacOS. I try to run
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swallowwly
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AFNI Message Board
Hi AFNI team,
I want to test the main effect of two factors (each has two levels, so it's a 2*2 design) and their interaction effect in every single subject (if it's a group analysis, it should be repeated-measure two-way anova). I read some posts before on this topic and I want to confirm here to make sure I did this correctly.
Experiment:
I have two factors, a and b, each has
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swallowwly
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AFNI Message Board
Hi AFNI team,
I'm running 3dDeconvolve on my dataset and it often got killed. The dataset is quite large. It has 32 runs of 10 min scanning, each run is ~400MB.
I run it on different computers and it seems not solely depend on the size of memory whether the process will be killed.
Here are my questions:
1) why is it that some computers have enough memory and hard drive but still
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swallowwly
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AFNI Message Board
Hi AFNI team,
In the afni result stats.$subj* files, we can always see the q and p values and set them as the threshold.
My question is: what's the q value fdr procedure used here? Is it Benjamini-Hochberg procedure or is it something else? Need the information for the paper method section.
Thank you!
-LW
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swallowwly
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AFNI Message Board
Hi afni team,
I found the gyrus/sulcus surface map is interfering with my dset map, even if I set the opacity to be 1...see the attached figure, it's making some yellow color to green when sulcus is beneath it.
Is there any way to avoid this?
Thanks!
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swallowwly
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AFNI Message Board
Hi pt,
The main reason for not using a non-flat map in this analysis is I need to settle the relative direction of each node to the cluster center.
But anyway, I found a way to solve the problem: I use the cluster info from a closed map and only use the coords from the flat map.
Thank you so much for your help, it was really useful advice!
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swallowwly
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AFNI Message Board
Hi pt,
Sorry that I have another question about this.
Calculating the distance is just one analysis we're doing. Another analysis we're trying to do, and this might actually requires a flat map:
We want to put the interested voxels within a cluster into a flat map and average the feature values through different axis that go through the center of the cluster.
I think this
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swallowwly
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AFNI Message Board
Hi pt,
I think you're right! This is exactly the thing I'm looking for! I didn't know this exist and thought distance of node pairs on a 3d brain is the x,y,z euclidean distance.
Can you send the link of the video? You mentioned a video but I didn't find it in your post.
Thanks so much -- this is very helpful!
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swallowwly
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AFNI Message Board
Hi pt,
Thanks for your input.
My research needs to do a topography analysis:
within each cluster, I calculate the feature distance and Euclidean distance between pairs of nodes and try to identify if there is a relationship between a physical map and a feature map. In this way, this flat map distance, which should correspond to surface distance, is more appropriate than the anatomical
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swallowwly
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AFNI Message Board
Hi pt,
Thanks for the reply.
I checked the flat map and it seems broken boundaries are the reason.
I have to use a flat map because I need to calculate the Euclidean distance between different nodes within a cluster. If it's not a flat map, such as a inflated one, the euclidean distance calculated between different nodes from x,y,z are not accurate.
If there is no other way in
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swallowwly
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AFNI Message Board
Hi AFNI team,
I was runing SurfClust on a flat map to extract cluster information from a dataset and got the following errors:
++ Notice SUMA_Make_Edge_List_eng (SUMA_MiscFunc.c:7799 @11:47:44):
Min/Max number of edge hosting triangles: [1/2]
You have edges that form a border in the surface.
Fatal Signal 11 (SIGSEGV) received
SUMA_Build_Cluster_From_Node_NoRec
SUMA_Find
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swallowwly
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AFNI Message Board
Hi Daniel,
Thanks for your message.
I've tried the 3drefit option but it didn't work.
When I fit the glm in afni, I used raw anatomy but not the SurfVol file. Could that be the problem?
I used 3dinfo to check SurfVol and my functional data and they seem to be in different spaces...
It seems I can only attach 1 file in this webpage and it has a limit in size and format...
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swallowwly
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AFNI Message Board
Hi Glen,
Thanks for the reply. I don't quite understand your suggestion. Are you suggesting I should run @SUMA_AlignToExperiment?
The surface model was generated for the anatomy for this experiment. I've tried using SurfVol and raw anat file both as the -sv but all have this problem of shifting.
Can you clarify a bit on your advice, please? Thanks!
-Lingyan
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swallowwly
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AFNI Message Board
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