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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 JW,
Sorry we did not get back to you on this.
It is preferable to make the masks based on the functional data. Alternatively, you could start with the brain mask datasets output by FreeSurfer and interect, fractionally intersect or take the union of them using 3dmask_tool.
What we like to do is create masks from the functional data intersected with those of the anatomical images, jus
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rick reynolds
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AFNI Message Board
Hi Michal,
Those are pretty long blocks, for which you might have to worry about being too closely modeled with slow baseline fluctuations.
Ignoring that, when event durations vary, we generally suggest the "duration modulation" approach, which uses a BLOCK-shaped basis function.
For a quick overview, the stimulus timing files should not just have onsets, but should have correspo
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rick reynolds
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AFNI Message Board
Thanks for the update, Giuseppe.
Sorry if it remains hovering in your mind, but hopefully it won't happen again.
- rick
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rick reynolds
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AFNI Message Board
These cases seem a little odd to me. For the prior one, since the dimension was a pure power of 2 and therefore not prone to rounding, I must wonder whether it was actually obliquity that caused the difference.
But having a different number of voxels listed is something else. It might be nice to post some before and after details, so we can get a better feel for the issue.
- rick
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rick reynolds
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AFNI Message Board
Hi Jenna,
The only special things to do for that are to pass the motion parameters via -regress_motion_file, and to pass any other (sets of?) regressors of no interest via -regress_extra_ortvec (and _labels). Beyond that, would you like to do blurring and/or scaling?
Just for a start, here is an example that processes like rest, but with no extra regressors of no interest for now.
It
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rick reynolds
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AFNI Message Board
Using 3drefit is a fine way to go, that or a related solution, like nifti_tool.
It might be good to revisit where these came from though, to get the TR set properly from the start. You would not want to require remembering to set that with all of the data coming in, it should already be in the NIFTI files.
Do you know how these datasets were created?
- rick
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rick reynolds
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AFNI Message Board
So the TR is not even in the NIFTI dataset? Is TR specified in an accompanying JSON sidecar?
- rick
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rick reynolds
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AFNI Message Board
Hi Jenna,
That seems fine from the view of projection. Blurring does not need to be done there, but it should be okay, too.
I gather you do not plan to do any censoring. That could be included if you wanted it.
It would also be reasonable to have afni_proc.py do these things, which would allow for a quality control HTML report to be generated.
But for just doing a projection and blur,
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rick reynolds
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AFNI Message Board
I think the issue for 3dvolreg is that the volumes have different obliquities. The volumes probably get registered well, but the output might not have the correct obliquity anymore.
For kicks, try this:
3dcalc -a ../localizer_results/ref.results/vr_base_min_outlier+orig -b 1.volreg_twopass \
-expr b -prefix 2.vr.twopass.grid
So 2.vr would have the data from 1.volreg, but should hav
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rick reynolds
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AFNI Message Board
HI Erik,
No, but you can use 1dcat, 1d_tool.py or whatever software to extract sets of columns into separate files. Then pass one file at a time using multiple -ortvec options, each with its own label. I suggest partitioning such regressors into a few sets, not just a single column per ortvec. But anyway, then you can give each ortvec its own label. You can pass them all as one set (as you
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rick reynolds
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AFNI Message Board
Hi Robin,
So the EPI localizer datasets are all in original, vr_base_min_outlier space.
Is this volume oblique, and is it the same obliquity as with the subsequent EPI runs? I would expect so. And if so, I do not see why the subsequent data would have the obliquity altered or removed, or was the same thing done to the localizer EPI? I would think no obliquity adjustment would be needed f
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rick reynolds
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AFNI Message Board
For reference, my 16 GB laptop cannot complete 10000 iterations, either. It gets about 2/3 of the way through (the randomsign step) before running out of memory and crashing. The number of threads does not seem to strongly affect this (some programs scale memory use by the number of threads, this does not appear to).
- rick
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rick reynolds
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AFNI Message Board
Hi Brady,
Paul has many good things to say of course. One thing to focus on is simply that your computer, in its current state, is not really good enough for that computation, even at 1000 iterations. Taking more than a day for 1000 iterations means it is already thrashing, spending most time swapping memory in and out because it does not have enough RAM for what it is doing. Doing 10 times
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rick reynolds
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AFNI Message Board
I expect the ve2a block of the APQC HTML report shows a failed alignment, too. Is that the case?
Do you have -giant_move included with -align_opts_aea?
Did you use Paul's suggested '-align_unifize_epi local'?
Please feel free to post the current afni_proc.py command.
- rick
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rick reynolds
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AFNI Message Board
And notably, as Paul referenced, please look at the images that have already been made as part of the APQC output.
From the subject *.results directory:
afni_open -b QC*/index.html
- rick
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rick reynolds
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AFNI Message Board
Sure, indirectly.
Add an option to your command like
-write_3dD_script RUN_3dD.tcsh
(and possibly include -write_3dD_prefix, though that is easy to edit).
That will generate a 3dDeconvolve command script that *assumes* all of the rest of the processing has happened, with a variable for a new output prefix.
You could possibly modify the regression options first, as it might be easier t
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rick reynolds
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AFNI Message Board
Hello,
From what you are saying the stim-active.txt file should not have those events at time 180 (time 180 should be for passive). As it stands, there are events at 0 and at 180, and each lasts for 180 s, which is the same as a single event that lasts for 360 s.
So stim-active.txt should probably look like:
0 *
0 *
0 *
Where the '*' characters are to make it look like &qu
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rick reynolds
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AFNI Message Board
Hello,
I will refrain from commenting on Matlab, but it looks like you don't have AFNI in your PATH (in bash), and so the attempted 3dcalc command (to generate an empty dataset) did not work.
Can you run AFNI programs from the shell? For example, what is the output (from a terminal prompt) of:
afni_system_check.py -check_all
- rick
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rick reynolds
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AFNI Message Board
That is right. To a fair degree, afni_proc.py does not know (or attempt to figure out) the number of time points that have any stim at all in them (which themselves would overlap, since many studies have multiple stimulations within a single TR (cue, button press, etc).
In any case, the number of TRs per stim (class) refers to the number of non-zero time points in the regressor.
For descript
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rick reynolds
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AFNI Message Board
This is a little strange, since it works for me and it shows the version during install.
I will send you direct email, and maybe we can do a quick zoom chat or something.
- rick
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rick reynolds
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AFNI Message Board
Great, so when you open a new terminal at this point, does afni work?
Does "afni -ver" show the version that you are hoping it shows?
- rick
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rick reynolds
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AFNI Message Board
You might have to open a new terminal or something, to source the startup file, depending on your shell.
Well, how about getting more details. What is the output from this?
~/abin/afni_system_check.py -check_all
Thanks,
- rick
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rick reynolds
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AFNI Message Board
Hi Lysianne,
Does that NIFTI image have a proper intent_code?
nifti_tool -disp_hdr -field intent_code -infiles MY_IMAGE.nii
If it does not, and so 3dClusterize cannot convert form p to an appropriate threshold, you can always provide a raw threshold yourself.
- rick
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rick reynolds
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AFNI Message Board
Hello,
I am not actually sure what the problem is, or in what way you see one.
What does "afni -ver" show after that?
- rick
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rick reynolds
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AFNI Message Board
Regarding still finding correlations in the ventricles, that is not a surprise. If you computed principle components within a ventricle mask, there would probably be 3-5 major signals, possibly including some BOLD. So regressing out a mean ventricle signal will not prevent the possibility of correlations within the ventricles (unless all of the ventricles had just a single signal).
Regarding
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rick reynolds
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AFNI Message Board
Hello,
Let me try to clarify some things.
0) What is your TR, and how many time points are there?
1) Are you trying to erode those masks twice? If so, maybe 3dmask_tool would be easier and more direct to use.
2) Do the regressor and regressor_deriv files look like valid time series?
3) Why do you think that the time series were not projected out?
4) Are you attempting to bandpa
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rick reynolds
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AFNI Message Board
Any program can monitor a file system or similar, and send data to afni. Dimon is such a program. It scans a directory, sorts images (, looks for errors), finds volumes, and then sends them to afni's real-time plugin. The plugin will do motion correction and averaging and such, and can then send motion parameters and ROI averages to an external program, such as realtime_receiver.py.
No
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rick reynolds
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AFNI Message Board
To answer your questions...
1) Yes, 1dplot uses a bottom to top ordering.
2) No, in dS, the S stands for Superior, and similarly for dL and dP standing for Left and Posterior. Those are independent of the ordering of the axes on disk.
- rick
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rick reynolds
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AFNI Message Board
Hi Philipp,
Actually, 1dplot plots from the bottom up.
- rick
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rick reynolds
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AFNI Message Board
By "full time course" I mean as much as you have, every time you run the computation, and it will grow over time. That could be done every single TR, as data comes in.
The plugin can send the new ROI average every time point.
At each TR:
- append the new ROI average to the previous "full" time series
- project motion/baseline from that full (current) time series
by
rick reynolds
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AFNI Message Board