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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 AFNI geeks,
I tried to install AFNI on a new iMac with macOS Monterey following the tutorial here. But when I run afni_system_check.py, I got the following message like this
QuotemacOS cannot verify the developer of “3dSkullStrip”
I have to manually authorize each program.
I've chosen the option which allowed installing programs from anywhere. Do you have a suggestion to fix
by
icupsy
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AFNI Message Board
Hi Taylor,
Thanks for the detailed explanation! Please see the attached F map. The whole experiment contains 4 conditions: auditory (A), visual (V), auditory-visual consistent (AVC), and auditory-visual inconsistent (AVI).
I just realized that a lot of TRs (10 out of 24) were censored for the visual condition, it might be just the data quality problem?
Xin
by
icupsy
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AFNI Message Board
Hi Taylor,
Thanks for the thorough explanation and Pythonic tips, I do redo the QC btw :)
Here are the QC images for ve2a and va2t.
Xin
by
icupsy
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AFNI Message Board
Hi AFNI experts,
We preprocessed task fMRI images and fit the GLM at the individual level. When we check the statistical maps for each condition at the individual level (p < .001), some statistical maps seem not to align the anatomical images very well. For example, in the attached files which belong to the visual condition, children just passively view the characters presented on the scree
by
icupsy
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AFNI Message Board
Something still strange:
When I click whereami in the Cluserize in the viewer, some warnings pop up in the terminal.
** Warning: Atlas CA_N27_PM could not be loaded.
** Warning: Atlas CA_PM_18_MNIA could not be loaded.
** Warning: Atlas DKD_Desai_PM could not be loaded.
** Warning: Atlas DD_Desai_PM could not be loaded.
** Warning: Atlas FS_Desai_PM could not be loaded.
The output of A
by
icupsy
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AFNI Message Board
Hi Daniel,
I checked my .afnirc file and I think the problem is caused by adding a template using the following commands:
AFNI_ATLAS_LIST "Haskins_Pediatric_Nonlinear_1.0,Haskins_Pediatric_Affine_1.0,CA_MPM_18_MNIA"
AFNI_ATLAS_COLORS Haskins_Pediatric_Nonlinear_1.0
AFNI_TEMPLATE_SPACE_LIST HaskinsPeds,MNI,TLRCThe output of AFNI_ATLAS_LIST:
After I remove these lines, the viewe
by
icupsy
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AFNI Message Board
Hi experts,
I open the afni GUI, set the underlay to TT_N27, then select the Draw Dataset option. The GUI suddenly crash and show some errors. By the way, I've seen the same error messages when I use "where am I" in GUI, but I can still get the information about the location.
Thanks a lot for the help!
Best,
Xin
These are messages popped up in the terminal and in .afni.
by
icupsy
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AFNI Message Board
I copied FS files from someone else, probably he did some other processings.
Good to know there is an easier way to do it!
Thanks a lot for the help and suggestions!
Best,
Xin
by
icupsy
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AFNI Message Board
Thanks, Rick!
I tried to keep either the "pial-outer-smoothed" or the "pial.nii" in the .spec file. The former version still throws 8 errors like "invalid surfaces, different # nodes ()" and the normal 'pial.nii' version works well.
I checked the 'recon-all.log' file and the FS files were generated by standard "recon-all" command.
by
icupsy
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AFNI Message Board
Sorry, I was wrong. I used "tcsh -xef proc.av |& tee output.proc.av" and the errors did not pop up. But when I just use "tcsh proc.av" to run the file, the errors are still there:
Errors:
Failed to read dset pb04.18001.lh.r01.surf.niml.dset
** ERROR: mri_read_ascii: can't read any valid data from file surf.smooth.params.1D
** FATAL ERROR: Can't read input
by
icupsy
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AFNI Message Board
Thanks, Taylor!
It did not throw any error after removing the tlrc-related commands. But it ended with "** surf name 6, 'pial': multiple matches: some paths" and there are many files start with "rm" in the results folder. Are these standard output files? I'm considering whether these are some temporal files that should have been deleted when the whole process
by
icupsy
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AFNI Message Board
Hi experts,
I try to run surface-based preprocessing on fMRI data. The script failed at reading input the surf.smooth.params.1D file and I check the file which turns out to be empty. I find a related topic on the board, it said that taking out some commands in SurfSmooth (-blurmaster and -detrend_master ) but it did not work.
I tried to fix it but I can't find more related information. Co
by
icupsy
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AFNI Message Board
Hi experts,
I used the app to install the AFNI on Mac but the uber_subject does not work even after I used fink and brew to install the pyqt. Could you please help me on that? And I also install the python following the instructions but it did not show python2 in the output of checking file.
Thanks!
-------------------------------- general ---------------------------------
architecture:
by
icupsy
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AFNI Message Board