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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, Sandra-
Hmm, OK. I don't know of one single command that can do that. You could inflate them separately/individually, while leaving the other ones there so that nothing overlaps...
Taking a step back, I'm a bit curious about inflating them differentially. Can I ask where the original ROIs come from (anatomical, FMRI, other...)? From purely tractographic considerations, the
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ptaylor
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AFNI Message Board
Hi, Sandra-
Does that mean that you have a single 3D dataset with 4 ROIs already in it, and you would like to differentially inflate them to be of the same (or at least similar) volume?
--pt
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ptaylor
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AFNI Message Board
Hmm, it appears to be pointing to a flat_namespace issue...
To be more certain, could you please copy+paste the output of the following here:
afni_system_check.py -check_all
?
--pt
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ptaylor
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AFNI Message Board
Hi, Abdullah-
The website contains *a lot* of helpful information, including tutorials with scripts to run, complementing the Bootcamp courses:
In particular, you can find recordings of previous Bootcamps under this Educational section:
...under both "AFNI Bootcamp Lecture Recordings" and "(Useful) Outside lectures" (the latter containing both Bootcamp teaching at M
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ptaylor
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AFNI Message Board
Here is some new work by Gang (again??) on analyzing data sets without the need for pesky multiple comparisons corrections:
How to Deal with Multiplicity in Neuroimaging? A Case for Global Calibration
And definitely worth checking out for anyone with a matrix appearing in their analyses/results.
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ptaylor
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AFNI Message Board
Hi, Joanna-
NIFTIs are perfectly acceptable in the AFNI software.
Personally, my usual "go to" for converting DICOMs is dcm2niix, which Chris Rorden & Co. have kindly contributed into the AFNI distribution itself (under the name dcm2niix_afni, so that it doesn't conflict with any other native version of dcm2niix you might have on your system).
--pt
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ptaylor
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AFNI Message Board
Jonathan-
Thanks for the dset.
However, it looks like that HEAD file contains no transformation information.
Since the history of that dset is also entirely missing, I wonder if it might have gone through some other software, perhaps, a process that would likely have purged that useful information?
--pt
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ptaylor
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AFNI Message Board
Hi, Stef-
The motion censoring criterion is based on the enorm (Euclidean norm) of the motion parameter values; that is calculated using volume-to-volume changes (the derivative of each motion parameter time series), so that I don't think one fixed movement between scans should result in a huge amount of censoring (assuming that that displacement wouldn't lead to large outlier value
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ptaylor
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AFNI Message Board
Weird. I will send you a PM to see about getting a header from one of those dsets to check out.
Out of curiosity, what is your AFNI version (afni -ver)?
--pt
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ptaylor
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AFNI Message Board
Hi, John-
OK, what did you specifically use in AFNI?
I just tried using the Nudge plugin, which gives a 3drotate command, and from the new dset named "dset_name" I can extract the applied rotation matrix with:
cat_matvec dset_name::ROTATE_MATVEC_000000
The inverse of that matrix can be calculated with:
cat_matvec dset_name::ROTATE_MATVEC_000000 -I
From using the AC-PC al
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ptaylor
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AFNI Message Board
Hi, John-
I have pinged the contributing author of the program-- Cameron Craddock-- at his google-scholar-verified email address, but have not heard a reply. I don't know if you might have better luck reaching out to him directly? Though, certainly having a reply on the Message Board would be nice for other users.
--pt
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ptaylor
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AFNI Message Board
Hi, Jonathan-
I don't think you mentioned how you did AC-PC alignment? If done with AFNI, that would help us locate where the information is; elif done in other software, well, I don't know that it would be recorded in the header.
-pt
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ptaylor
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AFNI Message Board
Yes, I would *definitely* check all public data as carefully as if I had just acquired it.
--pt
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ptaylor
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AFNI Message Board
Hi, again-
Also, as a quick follow up-- for a given dset name "dset_name", does this:
cat_matvec dset_name::ROTATE_MATVEC_000000
show 12 numbers?
--pt
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ptaylor
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AFNI Message Board
Hi, Jonathan-
How was AC-PC alignment done?
Does for a given dset name "dset_name", does this:
cat_matvec dset_name::WARP_DATA
show 12 numbers?
--pt
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ptaylor
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AFNI Message Board
Hi, Aviva-
Being BRIK/HEAD or NIFTI format will not matter to AFNI at all-- both are valid.
The main issue is the grid (origin, orientation, voxelsize, etc.). If the ROI was defined on some atlas somewhere, then it makes sense that it would probably be on a different grid. And indeed, you could use the same 3dresample command from above--with "-rmode NN"--with the final EPI dset
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ptaylor
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AFNI Message Board
Hi-
Splitting your 3dmask_tool command onto multiple lines so it is a bit easier to read:
3dmask_tool \
-inputs \
/data2/psychology/kimlab/fmri/studies/IDEA/infantcry/joelPPI/masks/rs_VTA_Adcock_mask+tlrc.HEAD \
full_mask.s21052+tlrc.HEAD \
-prefix rs_VTA_Adcock_mask.mask_inter \
-frac 1.0
... it seems you have two input dsets that you want to use together to make one mask.
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ptaylor
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AFNI Message Board
Hi-
You asked about the number of parameters being used; I am copy+pasting from a different MB thread here in reply (and slightly adding to it. The issue is counting degrees of freedom (DFs) as you build your model:
When you process a data set, you start with 1 DF for every time point you have (so, for N time points, you have N DFs). Every censored time point removes 1 DF (motion events
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ptaylor
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AFNI Message Board
Howdy-
1) The 3dinfo output is useful for diagnosis here, indeed. Looking at the 'extents' of each dataset--that is, the interval in space along the x-, y- and z-axes that the volume occupies--shows some interesting info:
### extents/FOV of the anatomical (units=mm):
R-to-L extent: -379.401 -to- -145.401
A-to-P extent: -407.182 -to- -138.233
I-to-S extent: 388.256
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ptaylor
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AFNI Message Board
Hi, Abdullah-
I wouldn't say bandpassing is default in AFNI. We have very few defaults, leaving those choices to The Researchers.
Not bandpassing shouldn't cause problems with ReHo calculations-- that parameter is a measure of similarity of time series in a neighborhood, and it is agnostic to the presence of bandpassing.
The "standard" range of LFFs (low frequenc
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ptaylor
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AFNI Message Board
Hi, Abdullah-
Yes, if you want to calculate RSFC parameters *and* censor time points (and the latter really is typically recommended), then care is needed.
If estimating RSFC parameters, and censoring, then you will have to *not* use "-regress_RSFC ..." in afni_proc.py. Instead, you will have to use the 3dLombScargle and 3dAmpToRSFC programs.
If you want to estimate fALFF or f
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ptaylor
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AFNI Message Board
Hi, Giulia-
I think that this part of the error:
** Failed "3dnvals -all /Users/giuliaavvenuti/Documents/H018/anatQQ.H018.nii"
** error in -tlrc_NL_warped_dsets p1: tlrc anat should be 1 volume,
but dataset anatQQ.H018.nii shows -1
means that afni_proc.py cannot find your anatQQ.H018.nii file. In that usage, 3dnvals will return the four dimensions of your matrix (3 spatial, one
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ptaylor
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AFNI Message Board
Okeydoke, sorry to be a buzzkill. It does sound like some other type of analysis might be more amenable with that particular data set.
--pt
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ptaylor
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AFNI Message Board
... and actually I have just been corrected by a *real* statistician, that the estimate of the standard error of the Pearson r for N time points is: 1/\sqrt(N-3).
That actually makes it worse: 1/\sqrt(5) ~ 0.45.
--pt
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ptaylor
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AFNI Message Board
Looks like you are on the cusp of runability: you need 9 time points.
I am not sure what correlation values of so few time points would mean. The stdev of a Pearson correlation value scales with 1/\sqrt(N-2), so for N=8, that would be 1/sqrt(6) ~ 0.4, which is preeeettty huge, consideration the Pearson r range is [-1, 1]. That means that your estimates with so few time points would be domina
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ptaylor
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AFNI Message Board
Hi, Edwin-
The default list size got reduced a while ago for readability, but full functionality do exist. You can set an environment variable in your ~/.afnirc to do this:
AFNI_ALLOW_ALL_PLUGINS = YES
See the more full description(s) of this and related env variables, excerpting from here:
--------------------------------
Variable: AFNI_ALLOW_ALL_PLUGINS
-------------------------
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ptaylor
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AFNI Message Board
Hi, Stuart-
Rick is on vacation this week, so I will try to step in to help, if I can. I will PM you instructions for sending your ~/.* files, so that I can take a look and see if something might be jamming up the works.
While those things will definitely need to be sorted out, it looks like you are driving AFNI to make images/snapshots of data. Please note that the @chauffeur_afni progra
by
ptaylor
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AFNI Message Board
Hi, ns-
Sounds like using 3dTcorrMap-- but do read the warnings about memory consumption/computational demands. You might want to try it with a smaller mask first.
using this output option:
-Zmean pp = Save tanh of mean arctanh(correlation) into 'pp'
-pt
by
ptaylor
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AFNI Message Board