Show all posts by user
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
In the GUI, instead of "Session", it is now "DataDir" (with "Switch" and "Read" next to the "DataDir" label).
You can start AFNI with multiple directories, as in
afni A B C
which will read data from the 3 directories named A, B, and C. Then you can switch among them with the "DataDir Switch". If you read in more than one directory,
by
Bob Cox
-
AFNI Message Board
For change 2), I'll add that you NEED to understand what you are doing to use -substatpar correctly. Otherwise, you will end up with a dataset whose statistical type and/or parameters are wrong, and then will probably be interpreted incorrectly (or worse).
by
Bob Cox
-
AFNI Message Board
New AFNI binaries, with this change (and others inspired in China) are now available.
by
Bob Cox
-
AFNI Message Board
你好
At our recent AFNI bootcamps in Shenzhen and Guangzhou, a few issues came up. Three changes have been implemented this week, inspired by discussions the the students there. Thanks go from me to the 100+ students we had in these cities for interesting discussions and questions. New AFNI binaries are now available with these updates. You can install them with the command
@update.afni.binar
by
Bob Cox
-
AFNI Message Board
There is no way to extract data from the .niml / .data pair created by 3dSetupGroupInCorr -- you have to extract data from the original input datasets. If they are not available, you can re-create them with program 3dExtractGroupInCorr.
by
Bob Cox
-
AFNI Message Board
I have fixed 3drefit to correctly implement the '-substatpar' option, which did not work when we were in Guangzhou. This fixed code has not yet been compiled into new AFNI binaries, though. I'm working on some other fixes that were suggested while we were in China.
The method to change the sub-brick in question would be something like
3drefit -substatpar 0 fizt -sublabel 0 Co
by
Bob Cox
-
AFNI Message Board
If you are also doing nonlinear warping to MNI space, then you can use the @SSwarper script, as in
@ SSwarper anat_sub007+orig sub007
Read the output of @SSwarper -help for the details
If you are NOT doing nonlinear warping, then the output of 3dSkullStrip -help has a bunch of information on how to make the skull stripping more or less strict.
by
Bob Cox
-
AFNI Message Board
I'm not sure WHY, but you could try a workaround.
On the 3dGroupInCorr command, add the option '-ah 127.0.0.1' to force the connection to use TCP/IP rather than shared memory (which is faster). This might work better.
I'm off to teach an AFNI bootcamp, leaving tomorrow (Fri Dec 1) morning, so I won't be available to answer questions for a while.
by
Bob Cox
-
AFNI Message Board
We are working on BIDS-ification of AFNI scripts, but who knows when it will be ready?
by
Bob Cox
-
AFNI Message Board
I didn't notice that you were using the -singletonA option. Neither ETAC nor Clustsim will work with that option, and I thought I had put in a test to make sure that type of situation would print out an error message and stop. I guess I did not do that (but will do it in a moment).
In your case, you want to test the mean of the -setB datasets against the constant 0.5. The only way to do
by
Bob Cox
-
AFNI Message Board
Without the data, it is difficult to say for sure. Guesses:
3dfim+ is very very old -- I don't know if it is still "good". Try 3dTcorr1D instead. Is it possible ANTS left a "hole" in the data when transforming it (that is, created a voxel with all zero entries)? It would be necessary to look at the transformed time series dataset (input to 3dfim+) at a location where t
by
Bob Cox
-
AFNI Message Board
How much data do you have in the 6 runs? The sample timing file you give has 53 events. Times 17 cases is about 900 betas to estimate (plus the 36 baseline betas). That is a lot! You need a lot of data to make that feasible.
by
Bob Cox
-
AFNI Message Board
The source code for 3dTsort.c now has the "-ranFFT" option, which will do phase scrambling of the FFT to produce a synthesized time series with similar statistical properties, but independent between voxel pairs.
by
Bob Cox
-
AFNI Message Board
I have put the slides about afni_proc.py scripting in a Google Docs folder, which you can access at https://goo.gl/uK4Tt7
You will also find some "real-life" scripts used for the work in a recently published paper. See the AAA.README.txt file in this folder for a description of the contents.
This link might also be helpful, as an introduction to shell scripting for AFNI: https:/
by
Bob Cox
-
AFNI Message Board
I have just added the "-random" option to program 3dTsort, which will randomly permute each voxel (independently) from an input 3D+time dataset. Source code is now in the AFNI github repository, and binaries will be available whenever we next rebuild.
Fortunately, I had a random permutation generator already coded up in 3dttest++, so was able to re-purpose that, and the rest was just
by
Bob Cox
-
AFNI Message Board
I have put a paper up on the arXiv: "Stability of Spatial Smoothness and Cluster-Size Threshold Estimates in FMRI using AFNI" http://arxiv.org/abs/1709.07471
The work therein was done in response to the paper by Karsten Mueller et al: "Commentary: Cluster failure: Why fMRI inferences for spatial extent have inflated false-positive rates"
http://journal
by
Bob Cox
-
AFNI Message Board
I have put a paper up on the arXiv: "Stability of Spatial Smoothness and Cluster-Size Threshold Estimates in FMRI using AFNI" http://arxiv.org/abs/1709.07471
The work therein was done in response to the paper by Karsten Mueller et al: "Commentary: Cluster failure: Why fMRI inferences for spatial extent have inflated false-positive rates"
http://journal
by
Bob Cox
-
AFNI Message Board
To answer your first question: only 3dREMLfit deals with temporal autocorrelation.
To answer your more philosophical question is more complicated.
In the past, 3dREMLfit was much slower than 3dDeconvolve, and computers were also much slower. The result was that there was a significant time penalty for using 3dREMLfit. And at the **group level**, there is very little difference between the g
by
Bob Cox
-
AFNI Message Board
When you save an image with the "Sav1" button, the popup has a field labeled "Blowup". This is a factor by which to expand the image. So set this to 4 or 5, and the image will be saved with 4 (or 5) times as many pixels in each direction.
However, to set the pixels per inch parameter in the saved image file header, if that is needed, you'll have to load the image file
by
Bob Cox
-
AFNI Message Board
You should put your AFNI binaries directory ~/abin FIRST in your path, which will help avoid problems like this.
Historical aside: program "count" was written before I ever thought of AFNI, for help in scripting. When I first started at MCW, I was appalled that everyone was manually writing out the filenames like X001, X002, ... X093, and then changing them manually for the next anal
by
Bob Cox
-
AFNI Message Board
30-60 minutes, as I recall (it's been a few weeks since I did this).
by
Bob Cox
-
AFNI Message Board
Do you have a newer iMac? That should be good, if you have enough memory. I'd say 16 GB, considering the OS (etc.) takes about 6-8 GB. If you run on a laptop, anything using 3dQwarp (such as @SSwarper) will take a long time.
I run this on my MacPro all the time, and have never seen a pipe error. However, I have 32 GB of RAM.
by
Bob Cox
-
AFNI Message Board
I wrote the @snapshot_volreg script to provide images to look at for this purpose. In your case, you would provide the (hopefully) aligned subject anatomy as one input dataset, and the template (TT_N27) as the other. See the output of "@snapshot_volreg -help"or https://afni.nimh.nih.gov/pub/dist/doc/program_help/@snapshot_volreg.html
by
Bob Cox
-
AFNI Message Board
Thanks for your kind words about AFNI. I designed the AFNI package (if you can call my semi-random process "design") to be flexible and allow for lots of different usages. For a user who wants/needs this diversity, and is willing to learn what it takes to use it -- a coding point of view, sort of -- AFNI is pretty useful.
Re-doing the GUI is a lot more work than you might think. I de
by
Bob Cox
-
AFNI Message Board
Paul points out I was somewhat terse in my reply last night. The outputs of this script are described when you type
@SSwarper -help
or when you follow this link: https://afni.nimh.nih.gov/pub/dist/doc/program_help/@SSwarper.html
The output files include the skull-stripped dataset in original coordinates, and as warped to the MNI 2009 template dataset. The transformation files needed for af
by
Bob Cox
-
AFNI Message Board
https://afni.nimh.nih.gov/pub/dist/doc/program_help/3dBrainSync.html
by
Bob Cox
-
AFNI Message Board
I have implemented the "BrainSync" algorithm of Joshi et al, as presented in their OHBM 2017 poster
https://files.aievolution.com/hbm1701/abstracts/38388/3966_Joshi.pdf
http://neuroimage.usc.edu/neuro/Resources/BrainSync
I also implemented my own permutation-only method of "synchronizing" 3D+time datasets, in the same program.
The goal is to take two 3D+time datasets (e.
by
Bob Cox
-
AFNI Message Board
I fixed a bug in 3dttest++ -ETAC, which caused the communication between 3dXClustSim and 3dttest++ to fail if multiple blur cases (-ETAC_blur) were NOT being used. Oops. Sorry about that. New binaries are compiling now, and should be available very soon.
by
Bob Cox
-
AFNI Message Board