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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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Hi Gang,
Thanks for your reply. The inputs are the correlation maps, yes, that I generated with 3dTCorrelate. I was under the impression that Cohen's d was for measuring the effect size of a difference between two groups? I am wondering if there is a way to measure an effect size for a quantitative variable in my model (i.e., head motion). Or is Cohen's d still the most appropriate f
by
ryctan
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AFNI Message Board
Hello,
I was hoping to calculate effect sizes for the continuous (quantitative) variables in a model I created with 3dISC. What would be the best way to go about this? Is there a certain measure of effect size (maybe Cohen's f^2?) that would be the most appropriate for the kind of regression it uses (linear mixed model w/ crossed random effects)?
Also -- is there a way to get an r^2 (c
by
ryctan
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AFNI Message Board
Hello,
I am trying to run 3dISC on a shared HPC at my institution. It took a while for us to get AFNI and the required dependencies installed, but it seems like it works now. Our research associate was able to run a basic 3dISC script of mine (just calculating the whole group effect without any covariates) on his account on the HPC, so we know that our installation process should have worked,
by
ryctan
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AFNI Message Board
Thanks so much for the suggestions! Looks like from 3dinfo that my data is in RPI not RAI. Weird! But the @xyz_to_ijk worked!
by
ryctan
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AFNI Message Board
Hello,
I am trying to access the value at a certain voxel using Nibabel. I have imported my AFNI image as a variable called "brik" and applied the get_fdata() to this to get the array containing all the values at each voxel coordinate. I.e.:
brik = nib.load('file.BRIK')
data = brik.get_fdata()
At first I tried to access the value at a certain voxel by using the coord
by
ryctan
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AFNI Message Board
Hi Gang,
Thank you so much for your suggestions/solutions! My code is working now, and I have been playing around with my model and I think I am close to figuring out what I need to do.
I really appreciate all the effort you and the rest of the AFNI team put into directly interacting with us, the users, when we run into problems!
- Ryann
by
ryctan
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AFNI Message Board
As a follow-up with some more information:
I tried to run the code again after removing the Age + Sex variables from the model and removing the -qVars 'Age,Sex' argument. It started to run the program and gave me "summary information of the data structure", except that instead of just having Set 1 be Subj1 and Set 2 be Subj2, set 1 was specified as Subj1 + my Age column and
by
ryctan
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AFNI Message Board
Hello,
I am trying to run my 3dISC script that includes my covariates and group factor levels. It keeps returning the following error:
updating R_LD_LIBRARY_PATH ...
Read 19956 items
Error in `[.data.frame`(lop$dataStr, , jj) : undefined columns selected
Calls: process.ISC.opts -> [ -> [.data.frame
In addition: Warning messages:
1: In process.ISC.opts(lop, verb = lop$verb) : NA
by
ryctan
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AFNI Message Board
Thanks for the quick reply! As I understand it, the first sub-brick is the image with the ISC correlation values, and the second sub-brick is the t-statistic map? It looks like the t-statistic map survives the FDR scrutiny... this is the one that matters when it comes to assessing statistical significance of ISC in the voxels, right?
by
ryctan
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AFNI Message Board
Hello,
I recently ran a very basic, one group ISC analysis on my data (58 subjects). I got the following warning:
*+ WARNING: Smallest FDR q [0 t] = 0.9999 ==> few true single voxel detections
++ Smallest FDR q [1 #1] = 4.36105e-13
I am a little confused as to what this means. What are the [0 t] and the [1 #1] referring to? When I am looking at the images in AFNI the q value stays
by
ryctan
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AFNI Message Board
Ran it with 5 subjects and it worked like a charm! Thanks!
Gang Wrote:
-------------------------------------------------------
> Ryann, try testing it with at least 5 subjects and
> see if you still have the same issue.
by
ryctan
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AFNI Message Board
Hi Gang, sorry, I did not see this post until now. I read it over and yes - that is pretty much exactly what I was hoping to do. I would be creating the parcellations myself through ICA, rather than using pre-defined set, but other than that, the methods described are the same as I was imagining. Good to know that that is possible. Also -- Part III was very interesting -- excited to see the futur
by
ryctan
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AFNI Message Board
Hi!
I am testing out the new 3dISC program with a few subjects and different inputs to get a feel for how it works. I am currently just trying to run a very basic 1 group ISC analysis on 3 subjects to see if I can get it running. This is my input:
bash-4.4$ 3dISC -prefix ISC -jobs 12 \
> -model '1+(1|Subj1)+(1|Subj2)' \
> -dataTable
by
ryctan
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AFNI Message Board
Hi Gang,
This is great news! Will be very helpful in my analysis.
I was wondering if 3dISC has the capability to do an ISC analysis based on ROIs rather than voxels? I was hoping to parcel my functional images into networks with ICA and to calculate the network-wise, rather than voxel-wise, ISC between subjects. Would I be able to use the images that have undergone ICA as inputs for 3dISC?
by
ryctan
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AFNI Message Board