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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, Giuseppe-
How about taking the log10(...) of the dataset before 3dBrickStat:
3dcalc -a DSET -expr 'log10(a)' -prefix DSET_LOG10
3dBrickStat -perclist 1 100 -perc_quiet DSET_LOG10
? That will just transform your range from [1.2326e-32, 5.58214e-07] -> [-31.90917784, -6.25319928], but it should be a one-to-one mapping, hence fine? And exponentiation with 10**(...) will
by
ptaylor
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AFNI Message Board
Howdy-
Hmmm, OK. I ran the following in the Bootcamp data (AFNI_data6/FT_analysis/FT directory) OK, and got the attached image:
3dTqual -range -automask FT_epi_r1+orig | 1dplot -one -stdin -png NAME
However, if I ran without the extension:
3dTqual -range -automask FT_epi_r1 | 1dplot -one -stdin -png NAME
... then I got the error you are seeing:
*** Can't open dataset FT_epi_r
by
ptaylor
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AFNI Message Board
Hi, Pawel-
Indeed, I would start with 3dAllineate---can always add nonlinear tweaks later, but also if this step fails badly, nonlinear wouldn't start well.
Note that 3dAllineate and 3dQwarp both have this opt:
-emask ee = This option lets you specify a mask of voxels to EXCLUDE from
the analysis. The voxels where the dataset 'ee' is nonzero
by
ptaylor
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AFNI Message Board
Ciao, Dante-
OK, let's chat about what can be done. I will email you offline.
--pt
by
ptaylor
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AFNI Message Board
Hi, Pawel-
With @chauffeur_afni:
https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/tutorials/auto_image/auto_%40chauffeur_afni.html
... you can set the crosshair presence and gap with:
-set_xhairs XX :specify type and/or existence of crosshairs in the
image (see DR: SET_XHAIRS).
-set_xhair_gap GG :specify gap in the crosshairs to the specified number
by
ptaylor
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AFNI Message Board
Hi, Carolin-
I would suspect that removing the trend would actually be useful, because you are looking to check for outliers before any processing; there are baseline fluctuations (low/slow moving trends in the data) that exist, and getting rid of those seems necessary before looking for outliers. Also note that with 3dToutcount, you can choose whether to remove trends or not, by selecting t
by
ptaylor
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AFNI Message Board
Hi, Jasmin-
There are a couple different ways to estimate RSFC parameters from resting state data. You *can* do it directly (and validly) with afni_proc.py, *if* you are not including any censoring within the processing. This is because the built-in method is Fourier-transform based, and an assumption for that is to have uniformly sampled data. When no censoring has been used, that would be
by
ptaylor
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AFNI Message Board
Hi, Matt-
Glad the article was of interest!
I think the main thing happening is noting the distinct usage of 2 AFNI programs for adjusting header information and datasets:
+ 3dresample is useful when the current header information is *correct* (in the sense that the data on disk is consistent with the header info), and when you change a header property like orientation, the data also gets
by
ptaylor
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AFNI Message Board
Hi, Christine-
I think if you put the following into ~/.afnirc, setting the environment variable:
AFNI_ATLAS_PATH = /usr/local/afni/bin
... that should do it. I tend to have both that and AFNI_GLOBAL_SESSION set to the location of my main directory of reference atlases and templates; in this case, that would mean also setting:
AFNI_GLOBAL_SESSION = /usr/local/afni/bin
there.
Can y
by
ptaylor
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AFNI Message Board
And, separately, note that you can use 'x', 'y', 'z' and 't' to represent spatial and temporal values, respectively, if you haven't used those to load in a dset (as well as 'i', 'j', 'k' and 'l' for their index analogue). See here:
https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/programs/alpha/3dcalc_sphx.html#c
by
ptaylor
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AFNI Message Board
Hi, Ian-
The output text suggests that the overlap of the two datasets is poor to start with. We can check that visually---what is the output of this:
@djunct_overlap_check \
-ulay AP1009B_anat_ns+orig \
-olay MNI_avg152T1+tlrc
... which might produce 2 images, if either of the ulay/olay contains obliquity in the header.
Also, can I ask the context that this is being run in?
by
ptaylor
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AFNI Message Board
Hmm, OK. What is the output of each of these commands:
# A
afni -ver
# B
@FindAfniDsetPath TTatlas+tlrc
# C
afni -no_detach -q -VAFNI_GLOBAL_SESSION=
# D
afni -no_detach -q -VAFNI_ATLAS_PATH=
?
thanks,
pt
by
ptaylor
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AFNI Message Board
(Posted on behalf of Bruno Averbeck in the NIMH's Section on Learning and Decision Making):
We are looking to hire a post-doc to work in the Laboratory of Neuropsychology, Section on Learning and Decision Making, in the National Institute of Mental Health:
https://www.nimh.nih.gov/research/research-conducted-at-nimh/research-areas/clinics-and-labs/ln/sldm
https://www.nimh.nih.gov/resear
by
ptaylor
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AFNI Message Board
Good to know, thanks for the update.
If it does appear to be an issue with the program(s), please just ping us back here.
--pt
by
ptaylor
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AFNI Message Board
Hi, Carole-
This may not be the source of the program's error (will defer to Gang on this), but I wonder if the same file should be used for two different subjects? The same exact file:
thresh_zstat13.nii.gz
... appears for both S1 and S2.
--pt
by
ptaylor
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AFNI Message Board
Hi-
I would agree that a single coordinate is often not enough for really summarizing a cluster accurately. We make the case here:
https://www.biorxiv.org/content/10.1101/2022.10.26.513929v2
... that the whereami functionality of looking for overlaps with an ROI atlas is a much more informative way to go. See in particular the discussion starting on page 17 of that draft ("One addition
by
ptaylor
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AFNI Message Board
No worries at all---better to ask (and always glad to see when people are doublechecking that what a program outputs matches their expectation).
Glad that sorted it.
--pt
by
ptaylor
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AFNI Message Board
Hi, Edwin-
Well, something is amiss because the code things you have 10 time points---that is what the "nFFT=10" item means. Can you please check the file? It would be looking for the number of rows in the file here.
If you need to transpose the file (to swap what are rows with what are columns), you could change the input file specification from:
ROIdump.1D
to:
ROIdump
by
ptaylor
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AFNI Message Board
Hi, Brady-
So, the option to use to specify "left is left" should look like:
-left_is_left YES
The "-left_is_left LIL" in the help file is using LIL as a placeholder for either YES or NO. Please let me know if changing "LIL" to "YES" fixes your issue.
(For me, "-left_is_left LIL" behaved like "-left_is_left NO"---but I will m
by
ptaylor
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AFNI Message Board
Great to know, thanks.
And, just for reference, I have now updated convert_cdiflist_to_grads.py to provide more useful and specific information to pinpoint where the "raggedness" is occurring, to aid in troubleshooting. That will be a part of the next AFNI build.
--pt
by
ptaylor
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AFNI Message Board
Hi, Price-
There is a line in your cdiflist text file where two columns have been merged:
-0.169-0.601 0.781
instead of
-0.169 -0.601 0.781
(line 14 in one-based counting)
If you fix that text file, then you should be good, methinks.
And me-also-thinks that you need to use the cdiflist if you have it, to have the correct gradients.
--pt
by
ptaylor
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AFNI Message Board
Hi, Stefano-
I generally use "make vastness" when I build, indeed.
Have you run:
afni_system_check.py -check_all
to check your AFNI setup on that system? That would be the best way to verify things.
--pt
by
ptaylor
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AFNI Message Board
Hi, Brady-
I think the question is whether one is applying blurring *to* data or estimating smoothness *in* data.
For estimating the smoothness in data, one wants to estimate more smoothly than a Gaussian approximation, because there will be inherent smoothness (=spatial structure of correlation) from the data itself, in combination with any further applied smoothing.
For applying blurri
by
ptaylor
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AFNI Message Board
Hi, Stefano-
Does running make without the parallel jobs:
make itall 2>&1 | tee out.make.txt
work? I wonder if the Makefile is not setup necessarily for parallelized building. I have never run with that "-j .." option.
--pt
by
ptaylor
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AFNI Message Board
Oh, and from spacing out the command, I think I see the issue: "-ortvec .." takes 2 parameters after it, not 1. From the 3dDeconvolve help:
-ortvec fff lll This option lets you input a rectangular array
of 1 or more baseline vectors from file 'fff',
which will get the label 'lll'. Functionally,
by
ptaylor
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AFNI Message Board
Hi-
A couple comments, but these won't really be solutions, likely, just features:
1) You have two backslashes, separated by a space, in a row at the end of your first line: "\ \"
I just spaced the text out a bit here (without that double slash):
3dDeconvolve \
-input /mnt/analysis/sub-${subjec
by
ptaylor
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AFNI Message Board
Hi, Megan-
Thanks for sending that information.
There is a Python error that shows up:
ValueError: Format 'jpg' is not supported (supported formats: eps, pdf, pgf, png, ps, raw, rgba, svg, svgz)
The bad news: the default package manager in Ubuntu 20.04 (Aptitude) distributes a version of Matplotlib, 3.1.2, that contains this error when trying to make JPGs:
I don't kno
by
ptaylor
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AFNI Message Board
Hi, Megan-
Re. #1: I think that is actaully the vstat block you are looking at and referring to (not the va2t) here, right? I will assume so in replying...
And indeed, the patterns observed here will vary depending on the task/stimulus and modeling. In the example you refer to, there was a very strong audio and visual task presented as a block design with many blocks---we would expect large
by
ptaylor
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AFNI Message Board
Hi, Rujing-
If you do your processing within AFNI, the history of processing of datasets is stored in the header in what is called the history. So, if you type "3dinfo DATASET" or more specifically "3dinfo -history DATASET". The history accumulates as the processing proceeds, so the n-th step in processing should have n processing commands stored in it. Note that this is
by
ptaylor
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AFNI Message Board