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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
Hi Brooke,
Note that the alphabetical ordering should be 1- 10- 100- 101- 102- ... 109- 11- 110- 111- ... 200- ... 2xx-
That is because '-' comes before '0'. So this does not match numerical ordering.
Try using Dimon and asking it to do the sorting:
Dimon -infile_pattern '*.dcm' -gert_create_dataset -dicom_org -save_details DET
Then you can look at the
by
rick reynolds
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AFNI Message Board
The peak of SPMG1 is 0.175441 ~= 1/5.7. So theoretically, all of the betas with SPMG1 will be 5.7 times those you would get with SPMG1(0).
That scaling will not have any effect on the group statistics, aside from computational truncation differences. It should only scale the group betas by that same 5.7.
GAM will have a real difference, as that curve has a different shape.
- rick
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rick reynolds
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AFNI Message Board
Hmmm, that "Comment:" text should not be there.
Do you have the text output from running the proc script, something like output.proc.SUBJECT?
If possible, would you be able to send that to me via email, along with the actual proc.* script?
Thanks,
- rick
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rick reynolds
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AFNI Message Board
There might be a problem before then. What is the output if you skip '1d'?
cat surf.smooth.params.1D
- rick
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rick reynolds
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AFNI Message Board
Great! Yes, either \ or | can be used as a line delimiter to make a multi-row GLT in 3dDeconvolve.
A proc script written by afni_proc.py will have the '\' characters, but that is appropriate for tcsh.
- rick
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rick reynolds
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AFNI Message Board
Hi Colm,
How are you running that script, via tcsh or bash. I think they will be different. bash might pass the '\' characters to 3dDeconvolve, which will treat them as line separators for the GLT, meaning they would have different rows. For example, consider:
-gltsym 'SYM: 0.25*SpatialBranch +0.25*SpatialDelay +0.25*VerbalBranch \
+.25*VerbalDelay -.25*Spatia
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rick reynolds
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AFNI Message Board
The atlas is probably a 'byte' dataset going from 0-255. So adding 1000 would not make sense.
Use 3dinfo to check the datum, and add "-datum short" to 3dcalc to convert it.
- rick
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rick reynolds
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AFNI Message Board
Note that atlases are generally based off of templates.
The CM of an atlas would be heavily weighted by the distribution of the atlas values, and it would not seem appropriate to base it on that.
The CM of a template would be more reasonable to use, however CM=0,0,0 is not so great there, either. Generally, templates have 0,0,0 somewhat near the AC, which does center the volume reasonably
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rick reynolds
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AFNI Message Board
Well, I would not say "best", it is just more complicated to have varying duration. But if they are all of the same duration anyway (across events and subjects), then it does not even matter (aside from being a little confusing if you publish the afni_proc.py command).
If they are the same duration D, I would probably go with BLOCK(D,1) for clarity, but that is up to you.
- rick
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rick reynolds
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AFNI Message Board
Hmmm, so the IM class is being modeled with dmBLOCK? I guess that should be okay, though I have never come across it, an extra complication...
- rick
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rick reynolds
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AFNI Message Board
Yes, you can pass a bunch of normal -stim_times files, as well as even a single -stim_times_IM.
The place to verify what is happening is in the regression matrix (which might be hard to plot, say). But even something like this can clarify the details:
1d_tool.py -show_group_labels -infile X.xmat.1D
You should still see the 3 runs of events (for the IM case) when plotting the X-matrix, bu
by
rick reynolds
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AFNI Message Board
Hello,
Actually, that is what Bob calls IM (individual modulation). It would be sufficient to pass 3dDeconvolve the cue timing (across all trials, as originally done), but pass it with -stim_times_IM (rather than just -stim_times). The output will have one beta per event.
Give that a try.
- rick
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rick reynolds
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AFNI Message Board
Hi Ian,
1. If the -global_times option is used first (in which case, ALL stim files should be global), then they will be read as global. Without that, 3dDeconvolve would warn about "times outside the range ..." and "unusable times follow".
And plotting those vectors from the X-matrix should show events going to the end.
Note that -global_times (or -local_times) shoul
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rick reynolds
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AFNI Message Board
Too bad... the mystery continues, sorry.
Could I see the output of : afni -get_processed_env
If you would prefer, please feel free to sent it via email, though maybe there is no need. It is up to you.
Also, please feel free to clear AFNI_GLOBAL_SESSION (env or .afnirc) and try again, just to see.
And to be sure, when you try again, would you first save the output from:
afni -availabl
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rick reynolds
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AFNI Message Board
Is there any chance that you have another 'afni' instance running under /usr/local/abin/bin?
What is the output from:
ps -C afni
If there are any other afni's running, please shut them down and try again.
- rick
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rick reynolds
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AFNI Message Board
This is odd, the problematic message appears to be:
RT: sending dataset rt.__001+orig with 2 bricks to AFNI, session /usr/local/afni/bin/
But it should be writing to the directory that you are in, not /usr/local/abin/bin.
Is there any chance that you have modified the demo.1.run script? Would you mind displaying your demo.1.run script?
And to be sure, exactly what directory is the scr
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rick reynolds
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AFNI Message Board
Hi Will,
I am a bit confused by this. It looks like it is trying to write AFNI datasets to the /usr/local/afni/bin directory. But if you would have run the script from there, it would have failed earlier.
There isn't a "cd /usr/local/afni/bin" command in your .cshrc file, is there? I am not sure what to think.
- rick
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rick reynolds
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AFNI Message Board
What is the output of:
1d_tool.py -show_mmms -infile 3dDecon_aCompCorr_rf/rf_matrix.1D
1d_tool.py -show_cormat_warnings -infile 3dDecon_aCompCorr_rf/rf_matrix.1D
- rick
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rick reynolds
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AFNI Message Board
Hi Brady,
Since only 5 runs would be passed to afni_proc.py, the timing files would similarly not contain any reference to a 6th run.
Assuming you still have all of the final betas, typically the only extra work would be to mention this in the paper submission, since that subject might be a little less reliable.
- rick
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rick reynolds
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AFNI Message Board
Actually, "make vastness" is identical to "make itall", and was presumably added without the author realizing that that particular target list already existed.
And 'totality' does that same thing as well, but also does cleaning on both ends.
Yes, that is how we generally build, without any parallelization. Parallelized cmake is only used as one of the circleci t
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rick reynolds
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AFNI Message Board
Thanks, Brady.
Actually, it is hardly worth running Dimon here, except that you could probably add the -order_as_zt option to fix the sorting.
I guess those images were run through an anonymizer though, as they do not seem to contain relevant sorting information. Is that the case?
Try adding -order_as_zt and see if that fixes it. I would expect so.
- rick
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rick reynolds
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AFNI Message Board
Dimon should always sort the images into a zt pattern. It the to3d command is not getting the files in the correct order (from the @filename order), it means the sorting is not working.
Would you please add the Dimon option "-save_details DET", run it again, and then send me email with perhaps a tgz attachment of the DET* output files? Or else you can just send the one that has &qu
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rick reynolds
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AFNI Message Board
Those patterns mean the same thing and work identically, either is good.
- rick
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rick reynolds
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AFNI Message Board
Given that, you should be able to run this using 3dDeconvolve, passing X and Z via -stim_file, and you can ponder whether -polort is appropriate and such.
Does that seem reasonable? I would be happy to ponder further.
- rick
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rick reynolds
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AFNI Message Board
Hi Giuseppe,
That looks like a linear model that could be solved with just 3dDeconvolve. Are either X or Z voxelwise? Presumably Y is, is that right?
- rick
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rick reynolds
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AFNI Message Board
The way the make files are set up, I think that you should not initialize CC via an environment variable like you are probably prone to doing with cmake.
I will have to revisit that, but try clearing CC (in your env) before the make.
Thanks,
- rick
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rick reynolds
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AFNI Message Board
Hi Stefano,
For compiling on a clean Ubuntu 20.04 system from a clean afni/src directory, I would expect it to be enough to:
# install needed build packages
bash afni/src/other_builds/OS_notes.linux_ubuntu_20_64
# and build
cd afni/src
cp afni/src/other_builds/Makefile.linux_ubuntu_16_64_glw_local_shared Makefile
make itall 2>&1 | tee out.make.txt
For nicities, install the
by
rick reynolds
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AFNI Message Board
Also, what is the output from:
3dinfo -tr -nt /mnt/analysis/sub-${subject}/func/sub-${subject}_scale.nii.gz
- rick
by
rick reynolds
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AFNI Message Board