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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,
Just an update that I I figured out what the issue was. My Subj column of my data table had unique names for each subject even though my design contains a within-subject factor. I overlooked the fact that in addition to specifying the within-subject factor I also need to make sure that individual subjects have the same name! Sorry for the trouble and thank you for your assistance!
Mich
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mjss
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AFNI Message Board
Thank you, Gang.
I'm running Version AFNI_22.1.09 'Antoninus Pius'. I was able to get 3dMVM to run if I remove the within-subject factor but it does not work when I try to run a model with just the within-subject factor, so that seems to be the culprit. Is there something I'm missing? I'm pasting a simplified version of my command below:
3dMVM -prefix GroupAnalysisWS
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mjss
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AFNI Message Board
Hi,
I am attempting to conduct a group-level analysis using 3dMVM. The design has 1 between-subject factor (group) and 1 within-subject factor (session). I would like to use 3dMVM because I have an unequal number of subjects in each group. I have followed the example set-up from the 3dMVM help documentation. When I attempt to run 3dMVM, it looks like the data structure and design is being read p
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mjss
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AFNI Message Board
Thanks, Gang. I have been attempting to do this but have yet to be successful. What AFNI processes rely on the brms package? E.g., is it possible to use afni_proc.py without this package?
Thank you,
Michael
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mjss
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AFNI Message Board
Hi,
I'm wondering if anyone has successfully installed all the required R packages for an AFNI installation on a mac machine with macOS Big Sur and R 4.1? I have been able to resolve other AFNI installation issues on macOS Big Sur documented here: but I am still struggling with the brms package. I am getting errors indicating that some of the dependencies required for brms are not being in
by
mjss
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AFNI Message Board
Hi Rick,
Thank you for these clarifications, I understand much better now. If the number of TRs per stim are based on stimulus response timing/BOLD response curves and therefore don't reflect the actual timing of each task condition, is there a way estimate how much actual scanning time has been censored per task condition?
Thank you,
Michael
by
mjss
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AFNI Message Board
Dear AFNI experts,
I am in the process of inspecting the QC html output from subject-level preprocessing and analysis of an fMRI dataset using afni_proc.py. I would like to obtain the percentage of censored TRs in each of my task conditions. However, I have noticed what appears to be a strange discrepancy in the values provided in the censor fraction warnings section of the output, which lead
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mjss
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AFNI Message Board
Hi Daniel,
The EPI dataset is 540MB in uncompressed nifti format. It contains 405 volumes with a voxel resolution of 2.5mm x 2.5mm x 2.5mm. Matrix size is 102x102 with 64 axial slices. I guess this is perhaps a larger than average matrix size?
Thank you,
Michael
by
mjss
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AFNI Message Board
Thanks, Daniel. I was able to use 3dcalc to convert the b0map float to integer. I'm still getting the memory error though. This is surprising because the EPI dataset is 500mb and this machine has more than ample disk space and RAM. So I'm not sure what that error message means.
Thanks,
Michael
by
mjss
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AFNI Message Board
Hello AFNI experts,
I am attempting to run epi_b0_correct.py to perform spatial distortion correction of my EPI dataset but I am running into some issues. I am attempting to execute epi_b0_correct.py following as per Example 1 in the documentation. My frequency dataset (fieldmap volume in rad/s) was created using FSL's FUGUE program.
Here is my command:
epi_b0_correct.py \
-epi_pe_
by
mjss
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AFNI Message Board
Thanks so much for your continued help with this. For each script, 3 image files are output (axial, coronal, sagittal) of a 3x3 slice montage without colorbars. The log files look nearly identical for both. I have copied the content for each below. One thing I noticed when looking at my afni_system_check is that although I am running Python 3.8 set up through Miniconda, it looks like the Python b
by
mjss
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AFNI Message Board
Hi again,
To follow up on this, I think I am noticing a similar error with some other scripts; for example when running the s00.warper script for the FT tutorial dataset on using @SSwarper. It looks like afni on my computer is reporting "WARNING: Bad drive AFNI result from 'SET_PBAR_ALL"..., which is similar to some of the warnings I get when running the afni.proc.py tutorial scri
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mjss
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AFNI Message Board
Part 2/2:
ERROR: QC_FT.NL/media/qc_11_regr_tsnr_fin.pbar.txt not found!!
++ My command:
@chauffeur_afni -ulay radcor.pb00.tcat/epi.ulay.r01+orig.HEAD -ulay_range 0% 110% -olay radcor.pb00.tcat/radcor.20.r01.corr+orig.HEAD -box_focus_slices AMASK_FOCUS_OLAY -cbar Reds_and_Blues_Inv -func_range 0.7 -thr_olay 0.4 -olay_alpha Yes -olay_boxed No -blowup 4 -set_subbricks 0 0 0 -opacity 9 -p
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mjss
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AFNI Message Board
Thank you for your help with this. I updated my afni binaries but unfortunately I'm still encountering the same problems. Here is the log from the redo_apqc script (copied in 2 parts because of the message character limit):
1/2:
michaelspilka% tcsh redo_apqc.tcsh
++ REDOing APQC
++ Going to re-run APQC in this dir only: /Volumes/Seagate/UGA/AfniBootcamp/AFNI_data6/FT_analysis/FT.NL.res
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mjss
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AFNI Message Board
Thank you. Please see below for the output.
Michael
michaelspilka% afni_system_check.py -check_all
-------------------------------- general ---------------------------------
architecture: 64bit
system: Darwin
release: 18.6.0
version: Darwin Kernel Version 18.6.0: Thu Apr 25 23:16:27 PDT 2019; root:xnu-4903.261.4~2/RELEASE_X86_64
distribu
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mjss
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AFNI Message Board
Dear AFNI experts,
I am attempting to follow the AFNI bootcamp tutorial but am encountering some errors when analyzing the FT data from AFNI_data6. I am able to run the sample s05.ap.uber script, and the resulting proc.FT script. However, this latter script returns some errors towards the end of the script during the APQC stage. Some of the QC files are missing (e.g., no .html file) and the @s
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mjss
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AFNI Message Board