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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 & AFNI team,
I was trygint o run 3dICC today, when the program stopped (immediately) with the following error:
Error in is.null(ss) || !length(ss) || ss == "" :
'length = 284' in coercion to 'logical(1)'
Calls: read.ICC.opts.batch -> parse.AFNI.args -> is.num.string
Execution halted
The full call was:
3dICC -prefix ICC/breathhold_o
by
smoia
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AFNI Message Board
Hi everyone,
thank you for all of your feedback!
It looks like I finally managed to compile it from source!
I unset CC and CXX, and run `make itall` without parallel jobs (pity, cause it takes a while, but it works!)
I also run rPkgsInstall, specifying R_LIBS as the folder where I installed R system-wise (/usr/lib/R in my case).
I didn't run a formal test, but R-based programs like 3d
by
smoia
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AFNI Message Board
Hi Rick, Daniel,
thank you both for your insight on the issue!
RE R installation: R was installed already before I started anything. Is there any environment variable I should set for the source build to know where to find it?
R (the environment call) is in /usr/bin, my R folder is in /usr/lib (/usr/lib/R is the R folder with its lib and modules subfolders). In one of my attempts I set cmake
by
smoia
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AFNI Message Board
Hello,
I hope I didn't miss a documentation page or a message in this board in starting this thread.
I'm trying to install a fixed version of AFNI in a container (apptainer), so that no matter when and where I run my analysis, it doesn't change. The apptainer contains other software too, and it's based on ubuntu 20.04.
I tried to use neurodocker, but I encountered a cou
by
smoia
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AFNI Message Board
Hello,
I was testing a couple of options to skullstrip some MP2RAGE data, and I noticed that if I don't deoblique the volume first, 3dSkullStrip changes the Qform and Sform in the header of the file - apparently rounding it up to 1 or down to 0.
See the attached files - the headers (skullstripped volume on the right) and the skullstripped volume (in blue-lightblue) over the original im
by
smoia
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AFNI Message Board
Hello Bob,
thank you for your answer! I'm going to empirically test the difference between the two cases for sure.
In the meantime, if I run 3dDeconvolve with all my regressors as "signal" and adding "polort", i.e.:
3dDeconvolve -input data.nii.gz -num_stimts 7 -polort 5 \
-stim_file 1 A.1D -stim_label 1 CO2 \
-stim_file 2 M.par[1] -stim_label 2 Motion1 \
-stim_f
by
smoia
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AFNI Message Board
Hi all,
I have a quick question about how 3dDeconvolve computes the T statistic and the F statistic of a regressor and the R2 of the model.
In particular, is there any difference between having a set of regressor specified as a baseline model (i.e. with -ortvec or -stim_base) versus specifying all the regressors as stimuli (i.e. with -stim_file but without -stim_base)?
As an example, I have
by
smoia
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AFNI Message Board