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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 Rick,
Suppose I have multiple columns of extra regressors in a file variable.txt, and use them as
3dDeconvolve ... \
-ortvec variable.txt var_name \
...
Is there a way to specify var_name such that each column in variable.txt has a different name in the X.xmat.1D file? As of now it seems they take the format var_name[0]#0, var_name[1]#0, ...
Thanks,
Erik
by
audachang
-
AFNI Message Board
Hi rick,
my input dataset are from the fmriprep preprocessing pipeline, and already in MNI152NLin2009cAsym standard space.
Best,
Erik
by
audachang
-
AFNI Message Board
It is handy to have -ClustSim natively implemented in 3dttest++
3dttest++ -ClustSim -prefix $results_dir/Flanker-Inc-Con \
-mask $mask_dset \
-setA Inc-Con
I wonder if there is plan to do the same for 3dMEMA?
Best regards,
Erik
by
audachang
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AFNI Message Board
Hi Rick,
I wonder if another error message immediately following the afni_python_wrapper.py command is relevant to this stream:
afni_python_wrapper.py -eval data_file_to_json()
gen_ss_review_scripts.py -exit0 -init_uvars_json out.ap_uvars.json -write_uvars_json out.ss_review_uvars.json
** guess tcat: failed to determine subject ID from pb00 files
** failed to guess subject ID
** failed
by
audachang
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AFNI Message Board
Hi Rick,
The latest update of afni_proc.py (version 7.39 on May 10) solved the problem. Thanks for taking care of it.
Cheers,
Erik
by
audachang
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AFNI Message Board
Dear afni experts:
I came across the attached errors when running the scripts generated by afni_proc.py. Apparently the error is from the following lines in the scripts generated from afni_proc.py.
# write AP uvars into a simple txt file
cat << EOF > out.ap_uvars.txt
out_limit : 0.15
copy_anat : \
sub
by
audachang
-
AFNI Message Board
Dear AFNI Experts,
From the following link, my understanding is that smaller normalized standard deviation is desirable in one's GLM design:
http://afni.nimh.nih.gov/pub/dist/HOWTO/howto/ht03_stim/html/AFNI_howto.html
"In a nutshell, the normalized standard deviation is the square root of the measurement error variance. Since this variance is unknown, we estimate it with the M
by
audachang
-
AFNI Message Board