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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
Results 1321 - 1350 of 2305
Hi, Steph-
While that blog is useful, a full processing description, from DICOM conversion through tracking, and including distortion correction with the recommended TORTOISE tools (also freely available from NIH, ) is available from here:
There are descriptions of outputs, and each program generates automatic QC images along the way, too. That goes hand-in-glove with the FATCAT_DEMO2 in
by
ptaylor
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AFNI Message Board
Hi-
Have you looked into using @SSwarper with afni_proc.py for setting up your FMRI processing? The latter program will set up all the intermediate alignments for you; it will manage several less exciting details of processing, while allowing you to specify your processing stream in detail.
If nothing else, you can run @SSwarper + afni_proc.py to see how afni_proc.py sets up the inversion
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ptaylor
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AFNI Message Board
Hi-
Are either of those data sets appreciably oblique?
3dinfo -obliquity DSET
You should be able to check your align_epi_anat.py results by overlaying the output file with the "_anat2epi*" suffix on it on the base EPI data set. How does that look if you open those up in AFNI?
--pt
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ptaylor
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AFNI Message Board
Hi, Irene-
My guess is that there is an environment variable that didn't get set during setup/installation.
Could you please copy+paste the output of AFNI's setup evaluator:
afni_system_check.py -check_all
?
thanks,
pt
by
ptaylor
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AFNI Message Board
Hi, Davide-
We have updated the installation of R on Ubuntu commands, and I think this will update/fix your R version. From here:
You can do this part:
curl -O https://afni.nimh.nih.gov/pub/dist/src/scripts_src/@add_rcran_ubuntu_18.04.tcsh
sudo tcsh @add_rcran_ubuntu_18.04.tcsh
which should update your R version, as well as any currently installed R packages.
Then, you should be a
by
ptaylor
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AFNI Message Board
Hi-
Yes, @SSwarper is a precursor step to afni_proc.py (that's a *good* thing-- if you have to update your processing and re-run, you don't have to redo the somewhat slow alignment). For this step, you reeeeeeeally want to use several cores/threads. This is where you really want OMP_NUM_THREADS set to be >1, if it all possible, and I provided script stuff for using SLURM explici
by
ptaylor
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AFNI Message Board
Hi-
Yes, @SSwarper can be run with any FMRI data (task, rest, naturalistic...).
To speed up (or, well, leverage as much speediness as possible), note that:
1) modern versions use the "lite" 3dQwarp processing-- so make sure you are using an uptodate AFNI.
2) It's parallelized with OpenMP, so deeeeeefinitely make use of that-- set OMP_NUM_THREADS on your system to be many
by
ptaylor
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AFNI Message Board
So, a volume has one value per voxel. Those discrete points in space, located within the volume's FOV, make up a data set grid. When you rotate the data set, what is its "new" grid going to be? It is the same grid as before, but with data values "rotated" through it? If so, you will have to interpolate the new data values in some way. That interpolation is resampling
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ptaylor
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AFNI Message Board
Hi, Stef-
I think you asked this question earlier, and I posted some response to that -- can you please check it out, and see if that is useful?
--pt
by
ptaylor
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AFNI Message Board
The minor upsamplign to voxel size seems both appropriate and convenient.
To deal with the anatomical grid/FOV: What if you used 3dAutobox (maybe with -npad to repad it a little) or 3dZeropad to shrink the FOV of your anatomical volume?
I am assuming you are not using the "tlrc" block to go to standard space? If so, you could use either of the above to shrink a copy of your te
by
ptaylor
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AFNI Message Board
To get the geometry matrix and dimensions:
3dAttribute IJK_TO_DICOM_REAL dset_name
3dAttribute DATASET_DIMENSIONS dset_name
To copy one matrix from a dset to another (but I don't think this is what you want to do for your data case here??):
# tcsh syntax
set obliq_matr = `3dAttribute IJK_TO_DICOM_REAL my_dset`
3dcopy other_dset other_dset_copy.nii
3drefit -atrfloat IJK_TO_DICOM_
by
ptaylor
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AFNI Message Board
Hi, Ruyuan-
Can you use "-master ANAT -mast_dxyz 3.0" (or whatever you want your final spacing to be)?
Note that typically in processing with afni_proc.py, individual transformations are calculated, and then concatenated before applying them to the EPI data. Is afni_proc.py not able to help with your processing needs?
--pt
by
ptaylor
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AFNI Message Board
Hi, Jung-
I don't know what "brightness" means.
And have you looked at the @chauffeur_afni command? It has a looooot of options to use for generating/saving images:
Here are a looot of examples online:
--pt
by
ptaylor
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AFNI Message Board
Hi, Stef-
Gang and I have chatted a bit about this, generating the following thoughts:
Your data set is a little bit different than the one from the Chen et al. work you have cited. In Chen et al., we were looking at a few longer clips of movies that were interspersed with rest. We spliced out the movie clips, and treated each as a separate run for processing (the clip presentation hadn
by
ptaylor
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AFNI Message Board
Hi, Jung-
I think this tutorial is very relevant for you:
In the beginning of that, some ROIs are made (just spheres) and put into a single volume-- you don't have to do that, since you have your own ROIs already. But the steps following that show how to generate surfaces for each ROI and show them in SUMA.
-pt
by
ptaylor
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AFNI Message Board
Hi, Jim-
OK. How about the following?
From how you described your question, I was assuming that you have the list of "x y z" coordinates in a certain orientation defined already (your "meta-analytic maxima coordinate(s)"). I call this file "coor_centers.txt", below. And you can put in the name of the file whose contents you are probing in this variable (in
by
ptaylor
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AFNI Message Board
Hi, Sungshin-
I would give @SSwarper a try on your original dataset.
It should produce a skullstripped+unifized version in the original space; a nonlinear transformation to standard space (e.g., MNI), and a representation of the brain warped to standard space. It can be a bit slow-- a couple hours on a laptop-- but if you can run on a multicore machine, you can specify the number fo threa
by
ptaylor
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AFNI Message Board
Ah, OK, if you have sub-regions/localizers that you are interested in, then sure, resampling makes sense.
It is possible you might consider multiplying that localizer mask by the full brain mask suggested before, to make sure that you have EPI information overlapping the localizer.
--pt
by
ptaylor
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AFNI Message Board
Hi, Ilaria-
So, while the reference template is used as a base for registration of the anatomical/EPI data, we generally tend not to recommend upsampling the EPI data all the way to that voxelsize. It doesn't create more information, and creates muuuuuch larger data sets. So, typically the voxelsize of the final EPI/errts/epits/stats dsets *do* have a different voxelsize/grid from the r
by
ptaylor
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AFNI Message Board
It is possible to calculate voxelwise quantities across the whole brain, and then view them or make calculations with them within specific ROIs or masks.
I will just guess that you are overlaying an anatomical on a background of ALFF values? (It wasn't clear from the description which dset was the overlay and which the underlay). Again, I don't see a problem with that-- ALFF values
by
ptaylor
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AFNI Message Board
Hello-
This question was originally asked on a separate existing thread, and was split into its own since it is a different topic. Because there were two starting points to the thread, to avoid confusion *this* question has been merged with the clarifying point here:
and so all discussions about this point should be carried on there.
Thanks,
pt
by
ptaylor
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AFNI Message Board
Hi, Davide-
This may look like a small thing, but from this manual about deb source files here:
... I wonder if you might need to remove the slash at the end of your ".....r-project.org/bin/linux/ubuntu/" string in the /etc/apt/sources.list file? I don't have that in mine, and it seems to suggest the blocks following it are treated differently (it might not matter; I'm
by
ptaylor
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AFNI Message Board
Hi, Davide-
From this line in it:
R version : R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
it seems that the R version has not been updated.
To check on the package manager sources file and see if it has been updated OK, what is the output of:
grep bionic /etc/apt/sources.list
?
(Note: you can also check your version of R by just typing R on the command line and r
by
ptaylor
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AFNI Message Board
Hi, Davide-
What is your output of
afni_system_check.py -check_all
now?
--pt
by
ptaylor
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AFNI Message Board
Hi-
Okay, you can check out this thread for explicit instructions on how to update your R to 3.5.3 on Ubuntu 18.04 here:
Well, I guess I can repost the instructions here so they are in a single post:
Remove your current R:
sudo apt-get remove r-base-core
Add the following line to the bottom of your /etc/apt/sources.list file *but also remove the underscores "_" as you do
by
ptaylor
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AFNI Message Board
Hi, Davide-
It's pretty hard to diagnose and remedy without more basic information about your system. Is it Mac or Linux (or Windows -> Linux)? What version of R do you have? If you could provide the output of
afni_system_check.py -check_all
that would probably provide most of the useful information.
My *guess* is that you might have to update your version of R to 3.5. to be a
by
ptaylor
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AFNI Message Board
Hi, Korann-
Well, that looks like it could just be the CSF in the midsagittal part of the brain, possibly, that is showing in the sagittal slice.
I don't know what viewer that is, but the representation looks a bit difficult to interpret. It would help to see it in the AFNI viewer (for familiarity's sake), preferably overlaid on the template you are using or on the anatomical tha
by
ptaylor
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AFNI Message Board
It looks like you might only have ten total subbricks in that dset, looking at the error message:
** ERROR: selector index 10 is out of range 0..9
AFNI, as many programming languages like C and Python do, counts starting from 0. So, for a ten item list, you can use indices 0, 1, 2, 3, ..., 9.
If you type:
3dinfo -nv DSET
that will tell you how many volumes in your DSET.
If you t
by
ptaylor
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AFNI Message Board
The tab autocompletion of AFNI programs is a different beast. Run:
apsearch -update_all
and when it is done running (shouldn't take very long), check the terminal-- there may likely be a message for you to copy+paste something into your current shell's ~/.*rc file. If not, just open a new terminal, and put an AFNI command followed by a space and a hyphen '-', and then h
by
ptaylor
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AFNI Message Board