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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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You may want to take a look at the script in this previous thread that includes an example ccalc command to include distance.
https://afni.nimh.nih.gov/afni/community/board/read.php?1,160717,160746#msg-160746
For some ideas on picking representative locations, see this poster:
https://afni.nimh.nih.gov/pub/dist/HBM2020/GlenEtal_FindingYourCenter_OHBM2020.pdf
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Daniel Glen
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AFNI Message Board
Hi Z.
My guess is to why this happens is there is some optimization that doesn't translate across MacOS versions. That's based on similar kinds of issues with illegal instructions on differing versions. We could compile these particular programs with no optimization or... we could compile for the more current MacOS. More recent OS's can also require code signing which we still do
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Daniel Glen
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AFNI Message Board
So that's weird. There is a related XQuartz/MacOS bug that seems to have disappearing windows. Cmd-tab twice sometimes brings lost windows forward. The posted fix seems to be with the MacOS to 13.3. Also update XQuartz to latest version.
https://github.com/XQuartz/XQuartz/issues/293
I may be able to test next week on a Ventura system, and try to explore this further.
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Daniel Glen
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AFNI Message Board
Based on the names of your datasets, you have used RAI oriented dataset. The xyz coordinates that are in the output are always in RAI. The input to the various box and ball input options allow you to choose whichever is more convenient. The dball and the xball will be equivalent with RAI input, so that's fine either way. If they weren't you can force RAI coordinates with -dball. RAI her
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Daniel Glen
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AFNI Message Board
I see an "illegal instruction" on an Intel Mac too, but it works with binaries built on the same machine. Okay, one more question (at least) - what version of OS are you using?
Can you try this copy of my 10.15 binaries and see if this works for you?
https://afni.nimh.nih.gov/pub/dist/tgz/macos_10.15_local_gcc_clang.tgz
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Daniel Glen
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AFNI Message Board
With a mask dataset as input, you would not use the -init_skullstr_off option. See the example 3 in the current @SSwarper help for how to use an external mask dataset as input. The mask provides a replacement for the initial skullstripping step. Voxels included in that mask should be included in the output datasets. The default nonlinear warping in afni_proc.py will work too, but it's a lit
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Daniel Glen
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AFNI Message Board
Are you running this on an M1 or M2 Mac?
Are you doing this in a Rosetta Terminal or the standard Terminal?
Which shell in the terminal? As an sh script within that shell?
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Daniel Glen
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AFNI Message Board
I am able to duplicate this - sort of. I don't get an error, but the long path doesn't return anything at all. The long path doesn't work under Rosetta emulation mode with our MacOS binaries, but both short and long paths work on binaries built from source on an M1 system. Are there any cigars for M1/M2 Apple system here?
Additional info - I do get an "Illegal instruction&q
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Daniel Glen
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AFNI Message Board
I did mean "show" with images, but okay. You don't mean a TSNR map, but just a single volume of PET imaging from some scan of a radioisotope that shows whole brain coverage? I am assuming FDG as the tracer then? Are you looking at the mean, median image, peak or something else?
The SNR is computed as the mean signal within the brain compared to its own standard deviation as a r
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Daniel Glen
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AFNI Message Board
Looks like you have made good progress. The initial skull stripping in @SSwarper is mildly aggressive by default, but it combines with the template alignment to create something more filled in. You can dilate the skullstrip mask or even manually fix the mask and feed that back into a 2nd run through of @SSwarper. You can change the options for the 3dSkullstrip command used in @SSwarper with -SSop
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Daniel Glen
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AFNI Message Board
My advice is skip the @Align_Centers step and the previous 3dWarp steps you had used. Try with just the @SSwarper and afni_proc.py command.
If you do keep these other steps, then try to add "-giant_move" to the -align_opts_aea line.
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Daniel Glen
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AFNI Message Board
Overall, I would probably let afni_proc.py handle all this. If you put the exact afni_proc.py command you used, then we can advise. The obliquity that you are working to remove is used to align the data and included in the transformations. The EPI output will be put onto the same grid as the anatomical but with a reduced resolution. One important advantage is the data has only one interpolation.
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Daniel Glen
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AFNI Message Board
This notice is part of our continuing AFDI.*
Recently, the AFNI team published our recommendations for quality control in FMRI.
https://www.frontiersin.org/articles/10.3389/fnins.2022.1073800/full
In this paper, we examined several FMRI datasets from open repositories. While we now pretty much expect a left-right flipping error in new data, we were surprised to find some subject brains a
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Daniel Glen
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AFNI Message Board
I'm going to assume you mean MacOS Ventura (13). I've seen something similar and strange years ago with El Capitan, and how it deals with multiple (2) monitors. Take a look at the advice from back then regarding the sometimes strange interaction of MacOS with XQuartz.
I haven't had a chance to try Ventura yet, but it also may be that Ventura has some problems with external m
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Daniel Glen
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AFNI Message Board
Can you provide the command you used and an image of the input dataset? Consider using @SSwarper to do similar kind of alignment to a template.
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Daniel Glen
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AFNI Message Board
Adding on to Paul's sage advice, the output from 3dWarp is different between the two datasets because the input is different - the two oblique angles are different. 3dWarp computes a bounding box for the output, so the boxes are slightly different sizes depending on the input grid and the oblique angles of the acquisition and transformation. You could supply a -gridset option that would serv
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Daniel Glen
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AFNI Message Board
AFNI does not run natively on iOS including iPads and iPhones, but there a few options.
1. Run on a Mac and extend display to iPad. You can use the "pen" button to draw.
2. Use afni remotely with an X11 server (Mocha) or a VNC server (Mocha-VNC).
3. NiiVue ROI drawing demo. This is a web-based Javascript application that works on all kinds of devices. We have been collabora
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Daniel Glen
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AFNI Message Board
A couple other ways:
# by atlas name, instead of dataset file name.
# Without -atlas, this shows all atlas indices and labels across all the installed atlases
whereami -atlas MNI_Glasser_HCP_v1.0 -show_atlas_code
# show the atlas structure, which is a little different than the labeltable
# this contains the center coordinates for each region and long names if they exist
3dinfo -atlas_p
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Daniel Glen
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AFNI Message Board
These kinds of differences are somewhat expected. Differences in the acquisition protocols make the contrasts different, but the anatomical variability is a bigger effect here, and more than the nonlinear warping can accommodate. While the overall alignment is very good in your images, you can see lots of small areas that don't match completely. The regions transformed from the meticulously
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Daniel Glen
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AFNI Message Board
Not with SurfMesh directly. You can instead use @SUMA_Make_Spec_FS or MapIcosahedron with higher -ld options for higher mesh densities.
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Daniel Glen
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AFNI Message Board
It seems worth mentioning here for future readers that the parameters from 3dvolreg could be applied with 3drotate instead (since 3dAllineate doesn't apply parameters the same way). Similarly, I would expect 3drotate would not handle the rotation parameters from 3dAllineate/3dWarpDrive appropriately. The matrix (matvec) inputs, on the other hand, should work similarly across the various AFNI
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Daniel Glen
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AFNI Message Board
Looks like you have figured all this out. Just to add a few tricks to your quiver:
1. 3dMean. this is a great program for combining lots of data with wildcards on the command line. Each dataset is loaded one at a time, so you are less likely to have memory issues. It doesn't provide as many statistical functions as 3dTstat though.
3dMean -prefix testschaef.nii.gz -mask_union ~/afni_sy
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Daniel Glen
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AFNI Message Board
I've never looked at this demo nor this data, and I'm no expert on retinotopy, so I'm hoping we can figure some of this out together. I don't see the same image that you show. The retinotopy results include both phase and power columns for the surface data. If I show phase and threshold by the power, I get something fairly close to the second image. (See attached) Except for t
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Daniel Glen
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AFNI Message Board
I don't know about mri_surfcluster, but I did find this info. The default should be in MNI305 space (the very original MNI space) by default now, but the options --fixmni and --nofixmni control whether you get TLRC or MNI space coordinate output. The header lines seem to switch between " TalX TalY TalZ" and "MNIX MNIY MNIZ". That program can be called directly or
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Daniel Glen
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AFNI Message Board
What program only outputs Talairach coordinates? All AFNI programs should be using whatever template space your data is in.
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Daniel Glen
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AFNI Message Board
Your version of AFNI is about 5 years old, and your version of R is current. Update AFNI to a current version, and use a version of R that's compatible with it. See the installation instructions here for the R install specifics:
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Daniel Glen
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AFNI Message Board
A few recommendations:
1. Use @SSwarper instead of @auto_tlrc. It will compute a transformation to an updated version, MNI152_2009_template_SSW.nii.gz (2009c asymmetric) of the MNI template using both an affine and a nonlinear alignment, and it will skullstrip the data too. The output can be used easily with afni_proc.py for an FMRI pipeline.
2. Use the MNI152_2009c template (MNI152_2009_temp
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Daniel Glen
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AFNI Message Board
Hi Chris,
We generally don't rotate DTI tensor values, only the positions, AFAIK. As Rick points out, it's problematic, and it probably won't be really right for a nonlinear alignment problems, which is how people would generally do an aligment nowadays.
We do take care of the somewhat related problem of transforming gradient vectors (1D lists of xyz vectors) for data that ha
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Daniel Glen
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AFNI Message Board
There doesn't appear to be an option to set the initial phase, and zero degrees is assumed. You should see this in the output files. You can modify the output as you like by adding or subtracting from the niml.dset output.
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Daniel Glen
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AFNI Message Board
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