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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
I'm glad you got this all figured out. The names for the supplementary atlases come exclusively from that CustomAtlases.niml file, so editing there should work. SessionAtlases.niml does something similar for programs to read the current directory. The atlases that are distributed are defined in the similar AFNI_atlas_spaces.niml.
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Daniel Glen
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AFNI Message Board
This may have to do with differences in the resampling/interpolation to the template. Try resampling first with 3dresample to the grid of the template and nearest neighbor interpolation.
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Daniel Glen
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AFNI Message Board
I can't quite see the full command, so I'll try to guess. If there is no master dataset, 3dUndump interprets the xyz coordinates in the input file as RAI (Right to left, Anterior to posterior, Inferior to superior). Otherwise, the xyz order matches the master dataset. It might be the text file you are using assumes the order of the master dataset. Instead of using xyz order, if you use
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Daniel Glen
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AFNI Message Board
You could try using to3d with the TIFF files as input. Dimon is meant mostly for DICOM files, not TIFF files, but it calls to3d to do the conversion to AFNI or NIFTI format. The netpbm package must be installed too, but that's typically part of AFNI installation. Note, not all TIFF files will be readable. It's sometimes useful to use something like ImageJ/Fiji for some of the formats. Y
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Daniel Glen
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AFNI Message Board
How did you generate the overlay dataset that you show here?
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Daniel Glen
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AFNI Message Board
FreeSurfer shouldn't be moving the original image. It regrids, but shouldn't move it. How are you visualizing this?
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Daniel Glen
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AFNI Message Board
AFNI should be showing all the volumetric files in "tlrc view", which refers to the data being in a standard space. You can see what space and what "afni view" a dataset is with this command
3dinfo -info -av_space mydset.nii.gz
The same command can be applied to many datasets at one time like this:
3dinfo -space -av_space -prefix ~/abin/HaskinsPeds_*.HEAD
HaskinsPeds
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Daniel Glen
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AFNI Message Board
There are also the -erode and -dilate options that can be useful.
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Daniel Glen
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AFNI Message Board
I've updated the various versions of this atlas - TT, MNI and MNIa versions of the macrolabel atlas.
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Daniel Glen
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AFNI Message Board
Sorry, I edited my previous comment to give some more details.
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Daniel Glen
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AFNI Message Board
Does the afni GUI start by itself? Is this problem limited to the Xvfb implementation that is used in the scripting?
Xvfb is used by @chauffeur_afni and other related scripts in AFNI. These are mostly written in tcsh. Configure the various shells to be configured to set the DYLD_LIBRARY_PATH to the path of library files that are provided with XQuartz. For example, in your .bashrc and .zshrc fi
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Daniel Glen
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AFNI Message Board
I've seen performance issues like this occasionally on recent Macs. In the Display preferences, set the refresh rate to 60Hz. In the XQuartz display preferences, set the number of colors to Thousands and restart XQuartz.
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Daniel Glen
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AFNI Message Board
You're very welcome, of course. Thanks for noticing this and letting me know this worked out.
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Daniel Glen
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AFNI Message Board
You would typically set that variable in your .bashrc file so that it is set everytime you restart a WSL instance. That is a configuration file for the bash shell. WSL versions 1 and 2 work differently, so you would set that variable for the one you are using. Most users have had better success with version 1 of WSL. Besides that WSL instruction page, there are a few message board posts like this
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Daniel Glen
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AFNI Message Board
Adding onto Paul's useful advice - the probabilistic atlases are generally not thresholded at all. The probabilities are typically a fractional overlap of some sort. The overlap is based on the template target for the multiple subjects and the alignment methods used to move all the subjects. The numbers actually used may be from 0-1, 0-100, 0-250, 0-79 for 79 subjects, ..., almost anything t
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Daniel Glen
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AFNI Message Board
That atlas is missing the center locations (see 3dinfo -atlas_points). I can add them with the following script. Try out the resulting dataset with the script and setting AFNI_ATLAS_COLORS to this "session atlas" for now ( setenv AFNI_ATLAS_COLORS TT_caez_ml_1.8 ). If it looks alright, I can update the standard distribution version. The atlas making script uses 3dCM to compute centers.
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Daniel Glen
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AFNI Message Board
Also, with a giant thanks to Rick, this task can now be accomplished with 3dTshift.
3dTshift -linear -prefix newideal.1D -TR 1 -tzero 0 -tpattern '@1D: 0.5' ideal.1D
This required a change in the code, so it will take a little while to get to regular distribution.
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Daniel Glen
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AFNI Message Board
As a test, what happens if you use "3drefit -oblique_origin" on a copy of the original dataset?
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Daniel Glen
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AFNI Message Board
The subbrick indices will be locked to integers, of course, but you could oversample to double the number of time points to be able to get to an index by 1/2 the original TR. Here's an example with a 3d+time dataset.
#!/bin/tcsh
set dset = epi_r1+orig
set nv = `3dnvals $dset`
@ nv --
set nlist = `count -digits 1 0 $nv`
set n2list = ()
foreach i ($nlist)
set n2list = ($n2list
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Daniel Glen
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AFNI Message Board
Sorry, lost track of the remaining questions. I believe the area is in mm2.
There is no simple tool for applying nonlinear warps to surfaces, but you can convert the surface to .asc or .ply and compute the new coordinates with 3dNwarpXYZ. Then you would have to save the new coordinates with the same triangles. Depending on the warp, it will likely make surfaces that flip inside-out and outsid
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Daniel Glen
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AFNI Message Board
If the data is very oblique, then the grid of the input anatomical dataset may not show any voxels once it is moved to the EPI grid. You may want to use -giant_move or provide a -master_anat dataset. For -master_anat, you can provide special strings like MIN_DXYZ, BASE or the name of a dataset that is approximately on the grid of the EPI dataset with the anatomical resolution. One way to do this
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Daniel Glen
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AFNI Message Board
Isn't this just a temporally shifted time series that could be accomplished by using the subbrick selectors as in this recent post:
You can add zeros to beginning or end, as you like, with 3dTcat, repeat the first and last elements or wrap around.
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Daniel Glen
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AFNI Message Board
For a very special April 1 edition in honor of the first live in-person (maybe) meeting in Glasgow, Scotland, we have exciting, new functionality.
This notice is part of our continuing AFDI.*
*AFDI
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Daniel Glen
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AFNI Message Board
That should work. Essentially, that is what is done internally for concatenations with nonlinear warps.
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Daniel Glen
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AFNI Message Board
Good to hear you have solved this. I am surprised the 3dWarp command didn't give the full grid on the output without the -gridset option.
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Daniel Glen
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AFNI Message Board
Interesting, as usual....
The rigid_equiv might work for this application too, but I think the nonlinear warp is a good idea to add onto the rigid transformation. You may want to limit the nonlinear warping to stop and start at moderate levels (~4).
I'm surprised that you're seeing an error like that. We regularly include nonlinear warps in native space and in template space with
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Daniel Glen
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AFNI Message Board
Hi Dante,
I've been good.
Sorry about the missing PDF. I think this is the one you have been looking for.
https://afni.nimh.nih.gov/pub/dist/edu/class_lectures/2020-03-NIH/afni15_atlas/afni15_atlas.01.pdf
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Daniel Glen
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AFNI Message Board
The grid of the output in align_epi_anat.py is controlled by the -master_xxx options. If you are using giant_move or ginormous_move, the grid is set to be on the base's grid but with the isotropic resolution of the minimum dimension of the input dataset by default. The master options override any of the defaults, and you get the grid on the output you want. I think in this case, the dataset
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Daniel Glen
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AFNI Message Board
There is some of the documentation here:
Let me know if that's not the latest one. I should be able to find it....
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Daniel Glen
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AFNI Message Board