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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 37
What is the proposed method in AFNI for clustering the correlation with a seed voxel?
3dTcorr1 doesnot mention what to do to choose cluster size so here is my workaround:
use 3ddeconvolve to get the R^2 of brain with the regressor being the seed voxel, get correlation coeficient from R^2. Use the residuals in 3dFHWMx and 3dclustsim to find the cluster size for a particular FWE.
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Ali_Ghazizadeh
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AFNI Message Board
I realized I should not use -nobucket because nothing was output in this case. removing that and keeping -cbucket option worked fine.
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Ali_Ghazizadeh
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AFNI Message Board
I have used 3dTcorr1D with column and row selectors like below and it executes without error. this usage is not mentioned in the -help so I was not sure if results are accurate. If correct would be good to add it to help
3dTcorr1D -pearson -prefix Corr+tlrc xset+tlrc'[0..$(2)]' Y.1D'{0..$(2)}'
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Ali_Ghazizadeh
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AFNI Message Board
I ran 3dTcorr1D and realized it outputs p values that are shown in afni. That is what I was looking for so I do not have to calculate myself.
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Ali_Ghazizadeh
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AFNI Message Board
I have many regressors I want to use in 3dDeconvolve (~72). There are all in a matrix .1D format. it is impractical to name them all using -stim_file option. Is there a way to pass the whole matrix in? I have been using -ortvec for passing a bunch of baseline regressors this way but for the main regressors I am not aware of such option.
In this case I am only interested in beta values (not t
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Ali_Ghazizadeh
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AFNI Message Board
Thank you my friends for suggestions and clarifications. I want to used 3dTcorr1D because I want to do multiple correlations at the same time ( i prefer to avoid for loops). signals to be correlated are concatenated 3D beta values from individual runs and a behavioral measure relevant for each run. so I do not need detrending.
In this case say I use z transform to calculate p values for correl
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Ali_Ghazizadeh
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AFNI Message Board
I need to find correlation of 3D+time with a time series I found function 3dTcorr1D which seems to do just that
2 questions:
1) I need to get the corrcoef along with the significances (or some stat that I can threshold for significance) in the description of function there is no mention of whether p values can be accesses ( e.g. looks like only 1 volume is returned per column of 1D input)
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Ali_Ghazizadeh
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AFNI Message Board
In the D99 template what is the origin of the DV coordinate? In the original atlas DV was with respect to interaural but looks like in the digital version it is with respect to anterior commissure. The same seems true for AP. would you please clarify?
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Ali_Ghazizadeh
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AFNI Message Board
thanks Rick,
another question: is there a way to change (increase) the contour line width when doing overlay in SUMA?
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Ali_Ghazizadeh
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AFNI Message Board
I have two questions about suma with multiple overlays
1. I am loading multiple Dsets which are 1 in some areas and 0 in others. The color map for all Dset is the same but SUMA shows them with different colors (maping of value 1 to a color looks different for different fg data sets) what determines this? chaning the order does not change this on the fly
2. is there a way to unload Dsets wit
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Ali_Ghazizadeh
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AFNI Message Board
I also need to move back time series data processed in Matlab to AFNI after importing data from 3dmaskdump and was surprised to find out 3dUndump can only do a single brik. It should be a simple code change to make it able to handle 3D+time. Is it possible to request this to be implemented? This would really facilitate interoperability between Matlab (or others) and AFNI
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Ali_Ghazizadeh
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AFNI Message Board
Thanks Bob and Gang, I will give them a try. Given that these methods are becoming pretty standard for resting state analysis, is there a plan to extend AFNI abilities in this regard near future?
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Ali_Ghazizadeh
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AFNI Message Board
Does AFNI have plugins to do ICA/PCA on resting state residuals and also for viewing resulting networks?
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Ali_Ghazizadeh
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AFNI Message Board
Thanks Rick, do you think this point is worth adding to the 3dAutomask and -automask option help in various functions?
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Ali_Ghazizadeh
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AFNI Message Board
Yes you are right. if I automask my errts time series I get zeros in the same regions. This time series is already masked coming out of 3dDeconvolve. So I didn't need to mask it again but I thought it doesn't hurt to redo automask, better safe than sorry right? not really.. thanks for the insight :)
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Ali_Ghazizadeh
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AFNI Message Board
Thanks Paul for the thorough explanation.
But what I wanted to know is that why 3dBandpass is setting some voxels to be zero at all times after filtering. I am using the errt time series which has fluctuation in all the voxels that are being zeroed in the output. I realize that if I don't use -automask option this does not happen. could this be a bug in the code?
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Ali_Ghazizadeh
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AFNI Message Board
I am using 3dbandpass for resting state analysis and I realized that the output time series is zero in lots of places. can this behavior be avoided?
below is what is printed to screen
++ 3dBandpass: AFNI version=AFNI_16.1.06 (Apr 19 2016) [64-bit]
++ Authored by: RW Cox
++ Data length = 7680 FFT length = 7680
+ bandpass: ntime=7680 nFFT=7680 dt=2.5 dFreq=5.20833e-05 Nyquist=0.2 passba
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Ali_Ghazizadeh
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AFNI Message Board
thanks Rick yes I realized I needed to refresh by moving/changing something in AFNI as you suggested. Ali
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Ali_Ghazizadeh
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AFNI Message Board
I am using vol2surf pluggin with WM and Pial surface. But toggling map function say from average to max, mode median etc is not changing the colors I see in SUMA. (i.e. not sure if SUMA is updating). When I change overlay I see somethings are being computed in the command line but still not sure if vol2surf has changed the way mapping is done or not.
I have set debug to 2 and I see this when
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Ali_Ghazizadeh
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AFNI Message Board
3dRSFC - 7 years ago
I get an error for specifying fbot ftop as 0.01 and 0.1 respectively in 3dRSFC. same bandpass works fine in Instacorr for the time series used. any insights? I am suspecting program may not expect in Hz even though the manual says so. error message below
++ 3dRSFC (from 3dBandpass by RW Cox): version THETA: AFNI version=AFNI_16.1.06 (Apr 19 2016) [64-bit]
++ Authored by: PA Taylor
++ Data le
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Ali_Ghazizadeh
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AFNI Message Board
I still see the name of the current directory followed by the file names even when I use afni -DAFNI_SESSTRAIL=0
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Ali_Ghazizadeh
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AFNI Message Board
I have the same problem with long names not showing and setting the variable in .afnirc or using afni -DAFNI_SESSTRAIL=1 does not seem to change afni behavior.
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Ali_Ghazizadeh
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AFNI Message Board
Thanks Paul, I was mainly interested to know if there is a place where I can enter exact values of rotation along axes instead of hitting keys multiple times to get to the view I like.
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Ali_Ghazizadeh
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AFNI Message Board
Is there away to punch in the exact values to rotate a surface along various axes in SUMA?
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Ali_Ghazizadeh
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AFNI Message Board
I have a recent version (Version AFNI_16.1.06) and you are right it was only going to 6 facewise (I have to learn how to count).
-neigh_upto_vert works great I have cute cubes now instead of pluses
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Ali_Ghazizadeh
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AFNI Message Board
Dilating a mask by 3dROIMaker ( and probably other afni functions) dilate it to the 18 neighboring voxels. I have single points of extrema that I want to dilate to cover 27 cube around it. Is there an option to do this?
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Ali_Ghazizadeh
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AFNI Message Board
Thanks so much for your responses. I can try TENT option but the issue is that even with the TENT we are finding the best fitted model to the data. Being able to just do an average BOLD (model free) would be very useful too, can we add such a capability to AFNI? A simple change to 3dTstat should be able to do the trick...
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Ali_Ghazizadeh
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AFNI Message Board
Thanks Daniel, let me be a bit more specific. Say I have a block design with rest and probe blocks interleaved. I want to calculate average BOLD from N TRs before the probe block to M TRs after. So for this I need to stack all runs time locked to probe block start and average. the output would be a 3D+time dataset with N+M+1 time points. I cannot figure out how to do this relatively basic thing
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Ali_Ghazizadeh
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AFNI Message Board
I want to calculate various statistics on 3D+time data but I want them to be computed according to a grouping vector with the same dimension as time axis. The grouping vector will tell the program which time points should be considered together for averaging, etc. The output would be a 3D + grouping bucket with stats for the first group in the first bucket and so on. Is there a way to do this in
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Ali_Ghazizadeh
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AFNI Message Board
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