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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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Hey Rick,
I think the mismatch there actually arose from my troubleshooting efforts. I tried loading the default afni module on our to see if the issue was specific to my user install prior to posting. I had the issue with both versions, but must have posted the error before unloading the default afni module. Aside from the missing R packages (I'll save that issue for a different post),
by
Nicholas Balderston
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AFNI Message Board
Hey Rick,
I think I solved the issue. I had the following line in my bashrc file, but it was commented out. I uncommented the line and it seems to be working now.
PATH=${PATH}:/usr/lib64
Not sure why it was commented, or what I broke by uncommenting, but I guess I'll save that for a future post.
-n
by
Nicholas Balderston
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AFNI Message Board
Hey Rick,
Thanks for the help. Here's the output.
$ afni_system_check.py -check_all
-------------------------------- general ---------------------------------
architecture: 64bit
cpu type: x86_64
system: Linux
release: 3.10.0-1160.21.1.el7.x86_64
version: #1 SMP Tue Mar 16 18:28:22 UTC 2021
distribution: C
by
Nicholas Balderston
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AFNI Message Board
Hey everyone,
I'm trying to run afni on the cubic computing cluster at penn. When I install afni, most of the command line tools work, but I get the following error when I try to run the GUI. Any thoughts?
afni: symbol lookup error: /cbica/software/external/afni/17.2.10/plug_3dsvm.so: undefined symbol: mcw_malloc
Thanks!
-nick
by
Nicholas Balderston
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AFNI Message Board
Quick update,
I tried working through the dependencies to install multcomp. I think I have traced things back to the following package: dcurver.
I gert the following message:
trying URL ';
Content type 'application/x-gzip' length 11173 bytes (10 KB)
==================================================
downloaded 10 KB
* installing *source* package ‘dcurver’ ...
** p
by
Nicholas Balderston
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AFNI Message Board
Hi everyone,
I am trying to run 3dMVM on a computing cluster, and I am running into the following error:
Error: package or namespace load failed for ‘lsmeans’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[]):
there is no package called ‘multcomp’
Error: package ‘lsmeans’ could not be loaded
Execution halted
However, when I run the following command,
by
Nicholas Balderston
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AFNI Message Board
Hi everyone,
I have analyses that were done in 3dMVM, which give me f statistics. I am trying to write a script that thresholds these maps using a p-value and a minimum cluster size, using the 3dclusterize command. I was always under the impression that I should use a 2-sided test for these f-values, because the underlying contrast could be bi-directional (i.e. exp > control or control >
by
Nicholas Balderston
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AFNI Message Board
Hi everyone,
I haven't gotten a reply, so I might ping someone from the AFNI team. In the meantime, I think I have found a workaround that works for me. At its core, I follow 3 basic steps.
run afni_proc on each run with minimal preprocessing using tedana to combine the echos. extract the "bad" component timeseries using @extract_meica_ortvec run the full afni_proc com
by
Nicholas Balderston
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AFNI Message Board
Hi everyone,
I've been collecting multi-echo data and using meica.py for some time now. I recently decided to switch to afni_proc, and have been having issues. I started by modelling my script from example 12b in the afni_proc documentation. However, tedana failed to reach convergence in about 1 in 3 subjects. This is much higher than if I use meica.py. I checked the usage recommendations
by
Nicholas Balderston
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AFNI Message Board
Hi everyone,
I am having trouble running meica.py with default options. Background... I am running analyses on the NIH biowulf computing cluster, which recently upgraded the OS and some software, which may be part of the problem. I am getting the following error, which seems to occur when trying to run the t2smap.py script. It only happens for one subject/run, but there doesn't seem to be
by
Nicholas Balderston
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AFNI Message Board
Hi everyone,
I think I have a potential solution to this, which is to use 3dLME, which can export the residuals, for the group level analysis. Afterward, I use 3dFWHMx to estimate the smoothness of the data, and 3dclustsim to run the monte carlo simulations. Here are example commands that I am using for my data. I understand that this is potentially a somewhat new approach, and that there are
by
Nicholas Balderston
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AFNI Message Board
Hi everyone,
We collected multi-echo data on an N-back task. We preprocessed the data using the meica.py script, and then performed the first level analyses on the denoised timeseries. However, when we extract the betas from load-related regions, we see mostly negative betas, which is not what we predicted. One possibility is that we are somehow overfitting our baseline during 3ddeconvolve. He
by
Nicholas Balderston
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AFNI Message Board
Hey folks,
I am planning to use 3dmvm to run an analysis on a bunch of beamformer volumes generated from MEG data. I'd like to use 3dclustsim to identify a minimum cluster size threshold, but I'm unsure about the best way to do that. Specifically, I have two questions:
1) Is it possible to output the residuals from my 3dMVM model, and if so, would it be appropriate to use these t
by
Nicholas Balderston
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AFNI Message Board
Nevermind, I think I figured it out. Sorry for the spam. -n
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Nicholas Balderston
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AFNI Message Board
Hey everyone,
I am starting a new multi echo study on 3TB at NIH. I am trying to get the meica.py script to run (on biowulf2), but am encountering some errors with the tedana.py script. Any ideas?
Here's the command I am using:
meica.py \
-e 18.4,39.5,60.6 \
-b 10s \
--OVERWRITE \
--daw=-1 \
-d 002.pre_rest_axial_epi.echo_001_dataset+orig,002.pre_rest_axial_epi.echo_001_dataset
by
Nicholas Balderston
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AFNI Message Board
Hey everyone,
Related to my previous post...
I am having trouble using 1dtranspose and 1d_tool.py on married timing files (e.g. 2.54*.094). Is there a flag that I am missing, or a better way to work with these files?
thanks!
-nick
P.S. I am currently using the following hacks, but it's not great if you have multiple columns...
#replace the newlines with tabs
cat file.1D | tr
by
Nicholas Balderston
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AFNI Message Board
Hey everyone,
Can 3ddeconvolve handle timing files where the entries are not ordered?
I am combining two conditions in my 3ddeconvolve script, and I am using cat (transpose --> cat --> transpose, to be precise) to combine the timing files. As a result, the entries are out of order. 3ddeconvolve seems to be running without error, but I want to make sure that it's working properly
by
Nicholas Balderston
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AFNI Message Board
One other detail, I tried changing the ICA dimensionality using the following flag "--daw=-1", but I get the following python errors. For reference, I am running this at NIH on biowulf.
Traceback (most recent call last):
File "/usr/local/apps/afni/current/linux_openmp_64/meica.libs/tedana.py", line 607, in <module>
acc,rej,midk,empty = selcomps(seldict,knob
by
Nicholas Balderston
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AFNI Message Board
Hey folks,
I'm running into this error with one of my subjects:
"No convergence after 5000 steps"
Here's my command.
meica.py \
-e 12,24.48,36.96 \
-d 024.run4.12+orig,024.run4.24.48+orig,024.run4.36.96+orig
Any ideas to get me started troubleshooting this one?
thanks,
-nick
by
Nicholas Balderston
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AFNI Message Board
Ok, that makes sense to me now.
I think I was confused because I was imagining that the temporal discontinuities would be accompanied by a shift in the scale of input data.
Thanks!
-nick
by
Nicholas Balderston
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AFNI Message Board
Hey Gang,
Thanks for the quick reply!
However based on your reply, I am not entirely sure I understand how 3dTcorrMap works.
As I understand it, for each voxel the program computes the correlation across the time domain, and then sums across the space domain. If this is the case, then the temporal discontinuities would create jumps in the data, thus increasing the shared variance.
by
Nicholas Balderston
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AFNI Message Board
Hey Folks!
I was thinking about using 3dTcorrMap to look at global connectivity during 2 different task conditions, which occur during alternating ~2min blocks. As I understand it, 3dTcorrMap can give you the global connectivity for each voxel, given a timeseries.
My question is:
What's the best way to generate the 2 timeseries when the conditions are alternating?
I can imagine
by
Nicholas Balderston
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AFNI Message Board
Hey folks,
I'm trying to use 3dNwarpApply to combine multiple transformations in a single step. I'm using the version compiled on Dec 5 2014, and I think the recent update might have broken my script. Previous versions of the script worked, now I am getting the following error.
Processing -nwarp ** ERROR: Cannot read affine warp from file '018.base_PLUS_al.1Dparam.1D
by
Nicholas Balderston
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AFNI Message Board
Hey folks,
I am putting together some preprocessing scripts based on multiecho EPI data. In addition, I am trying to use forward and reversed phase-encoded indices to correct for EPI distortions. Here's the question...
Given that I am working with skullstripped data, I find that as I add steps to my alignment process, I get progressively more noise outside of the brain. Is this true no
by
Nicholas Balderston
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AFNI Message Board
Hi everyone,
Here's a judgment question.
I'd like to know whether or not it is justifiable to convert betas (from 3dDeconvolve) to z-scores? Here's what I did.
First I took each subject's set of betas, and calculated the mean and standard deviation across conditions.
3dMean -prefix ${subject}.mean.beta.blur `ls ${subject}.?.?.beta.blur+tlrc.HEAD `
3dMean -sd
by
Nicholas Balderston
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AFNI Message Board
I would also be interested in attending an AFNI bootcamp. -nick
by
Nicholas Balderston
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AFNI Message Board