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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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I wouldn't use the term "baseline" when discussing the mean value of the errts time series.
The linear regression step of a time series basically asserts that a time series can be written as the sum of 1 or more provided components, each with a to-be-estimated coefficient (or beta weight); finding those coefficients is the point of the regression step. The sum of each compone
by
ptaylor
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AFNI Message Board
Hi, Philipp-
The errts file is a residual from regression modeling. It should have mean zero. During regression, the baseline is modeled, and the baseline typically includes the mean value of the data.
When using the 'scale' block, the data prior to the regress block are scaled to have mean=100 and a (generously) capped range of [0,200]. This scaling is done on per voxel basis
by
ptaylor
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AFNI Message Board
Offhand, I don't really use global signal so I am not sure and don't have an example handy, but it is useful to note that afni_proc.py creates a script (default name: proc*) so that these things can be investigated by the user in detail. The script is even commented.
If you add your specific AP command here we could look at it to see, as well.
--pt
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ptaylor
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AFNI Message Board
It's kind of a philosophical question---what is the region of interest supposed to represent? Strictly speaking, a region is a region if you want to present it as a thiing that passed a certain threshold. Do you want the subregion for more descriptive purposes?
--pt
by
ptaylor
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AFNI Message Board
Howdy-
OK, that is a long time series. The option for controlling the degree of polynomial in the regression model is this, which explains the default degree chosen (based on the run_length value, which is the total time of the EPIs), as well as how to adjust it and use the "-regress_bandpass .." option to do some baseline capturing, itself:
-regress_polort DEGREE : specify the
by
ptaylor
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AFNI Message Board
Hi, Danny-
Running "afni_system_check.py -check_all" will tell you pretty clearly if everything that is needed, is installed. One decision point that could be kicked on down the road could be the R-based programs, which are mainly for group level processing. But it would probably be best to have all the other checks passing, to avoid any weird and/or possibly subtle issues.
--pt
by
ptaylor
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AFNI Message Board
Okeydoke. Just to note the Ubuntu 20.04 installation instructions are here:
https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/background_install/install_instructs/steps_linux_ubuntu20.html
For the GSL, I would run this to install it:
sudo apt-get install gsl
... and then this to link it (sigh):
sudo ln -s /usr/lib/x86_64-linux-gnu/libgsl.so.23 /usr/lib/x86_64-linux-gnu/libgsl.so.19
For
by
ptaylor
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AFNI Message Board
Also, the program *should* exit at the first failure. I see that the status checks weren't in optimal places, and I have tweaked that in the program now, so future versions should be easier to diagnose.
Thanks for bringing that issue up.
--pt
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ptaylor
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AFNI Message Board
Hm, what is the output of
afni_system_check.py -check_all
?
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ptaylor
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AFNI Message Board
Hi, Jewel-
That does seem like a high order of polynomials. Is the time interval of that set of EPI data (total number of time points times TR) quite long?
Maybe a maximum polynort number could be specified, and a high pass filter used to remove the baseline in this case.
What is the full afni_proc.py (AP) command, and do you have a the tee'ed log file of terminal text for the co
by
ptaylor
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AFNI Message Board
Hi, Danny-
Hmm, OK.
First to note: those "Step ..." references are just to help pinpoint in the code which step failed, for someone looking through the @SSwarper tcsh script itself. That particular step is inverting a warp... Do you happen to have log file of the full terminal output from running that command?
Also, if I shared instructions, would you be able to send me t
by
ptaylor
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AFNI Message Board
Thanks, Sam, that is a useful link (and many of those replies do refer to @SSwarper directly).
The case of using a "component" dataset which should ~easily automask to punch away the background was what I was going to lean toward suggesting---the Case #4 I had listed in that other thread.
--pt
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ptaylor
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AFNI Message Board
Hi, Jenna-
I am not aware of a tool to do this. The hardest part is picking a single point from each ROI (which is an extended volume, potentially of wildly weird shape) from which to calculate distance? I imagine center of mass or some kind of central point would be used, but consider how different distance might be interpreted, whether it was between two spheres or two octopuses with tenac
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ptaylor
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AFNI Message Board
Hi, Philipp-
Is that perhaps a quasi-synthetic T1w volume, made by combining multiple separate echos, and therefore the noise background is relatively elevated? If so, do you have the original component volumes?
--pt
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ptaylor
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AFNI Message Board
Hi, jef-
There are two issues here:
1) Is the left of the image also the leftside of the displayed brain (default convention) or the right side (switchable)?
2) Are x-values to the left of the coordinate origin positive (RAI-DICOM notation) or negative (LPI/SPM ordering)?
Each of these is a convention, and you can choose to set what you prefer. Each of these can be changed either tempora
by
ptaylor
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AFNI Message Board
There really isn't a good way to have multiple overlays in the AFNI GUI.
You could multiple the stats map DSET_STATS by the region map DSET_ROI, adn show that:
3dcalc -a DSET_STATS -b DSET_ROI -expr 'step(b)*a' -prefix DSET_STATS_IN_ROI
... and then use DSET_STATS_IN_ROI as the overlay.
A somewhat cheating method might be to concatenate the stats volume and the ROI one, an
by
ptaylor
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AFNI Message Board
Hi-
The fat_proc_map_dti program uses affine registration, so bringing data from a subject's own anatomical dataset to the DWI that has been aligned to it makes sense with that level of warping.
To bring ROIs from a reference template to a subject DWI/DTI dataset would likely require nonlinear alignment for reasonable accuracy; once the transformation/warp has been estimated, one can
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ptaylor
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AFNI Message Board
Hi-
Just to check if I have this correctly: you have an anatomical underlay dataset, and the overlay is a single ROI, that is a binary mask. Do you just want the outline of the ROI, as well as the ROI shown transparently?
Or do you have an ROI region with stats values in it, for the overlay?
--pt
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ptaylor
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AFNI Message Board
QC! Near and dear to our hearts! Let's fix this crash!
There is some suggestion perhaps in that crash message, but to be sure can we start with checking the system setup---could you please copy+paste the output of:
afni_system_check.py -check_all
?
--pt
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ptaylor
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AFNI Message Board
Hi, Alex-
Module loading is certainly reasonable on an HPC system---to some extent, it is probably expected. You can likely even add those things to your scripts to run. Depending on how that system operates, the "scripts_biowulf/" directory might be useful, because it scripts HPC features like swarming jobs and using a temporary scratch disk to write to and copy back from. How di
by
ptaylor
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AFNI Message Board
Hi again-
I should have been more clear in my initial reply that I was specifically referring to generating a separate APQC for that new output. I have edited my reply now to be more precise. Rick has commented about the other aspects.
--pt
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ptaylor
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AFNI Message Board
Hi, Ian-
There isn't a mechanism for generating a new APQC HTML from that kind of rerun that generates a separate output in the results directory at present, unfortunately.
--pt
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ptaylor
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AFNI Message Board
Cool.
You can set up miniconda/conda even on an HPC, since it doesn't require sudo permissions. Here are notes related to conda and AFNI specifically:
https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/background_install/miniconda.html
Basically, you create a directory of useful programs with dependencies in a very self-contained directory, say in your subfolder of your home directory.
by
ptaylor
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AFNI Message Board
Hi, Philipp-
"ijk" refers to integer-based indices for locating oneself in an ordered collection, like a list/array. These numbers are have no units, and go from 0,.., N-1, where "N" is the size of the collection along the given dimension. These are independent of voxel size.
"xyz" refers to physical coordinates of the dset, each of which has units of millime
by
ptaylor
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AFNI Message Board
Hi, Philipp-
Thanks for that explanation.
When you refer to the Scaefer-Yeo dataset, I guess that means that atlas (ROI map of regions), right? That is different than a template.
But the main point is you want to use this ROI information with the errts file (or more specifically autocorrelation derived from errts file) information? Can you please check that your Resample_Yeo7N_1000
by
ptaylor
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AFNI Message Board
Hi, Alex-
Wow, that is embarassing that that message appears in the help file from our build system... I will check that out, thanks for pointing that out.
So, that RetroTS.py program does have pylab as a module dependency. I would have thought installing matplotlib would install that as well, in most situations. Could you perphaps copy+paste the output of:
afni_system_check.py -check_
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ptaylor
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AFNI Message Board
Hi, Philipp-
The output:
1 1 1 1 1 ACW_Awake_Global.nii
1 1 1 1 1 Resample_Yeo7N_1000ribbon.nii
... suggests that these two files are on the same grid.
I wouldn't do any ad hoc coordinate adjustments in Python. That would mean that header information could easily become incorrect, and that is possibly happening here? I am not sure---but I don't see any reason to int
by
ptaylor
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AFNI Message Board
Hi, Philipp-
That first dataset has not been entered correctly, since the program cannot find it, hence the NO-DSET messages. Please make sure that is the correct name and/or directory---path information can be included to locate it, too.
--pt
by
ptaylor
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AFNI Message Board
Hi, Colm-
I suspect that using @chauffeur_afni:
https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/tutorials/auto_image/auto_%40chauffeur_afni.html
would simplify your life here. It automatically makes sets of axial, coronal and sagittal images. It can make montages, and/or you can specify slice locations. You can specify ulay and olay ranges at the command line. You can combine it with 2dc
by
ptaylor
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AFNI Message Board
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