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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 think I've seen some mysterious issues like this on high-use network drives, and some sleep never hurt anyone. I suppose a programmatic pre-read sleep might help or a post-write sleep. What program wrote that dataset that becomes the input for the 3dcopy? You could wrap 3dcopy in a script to include a delay before and after, maybe making the amount of sleep different if the input and outpu
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Daniel Glen
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AFNI Message Board
We don't use the Talairached version of the MNI 2009c dataset, but we do have the MNI 2009c in MNI space. The Desai atlases provide a maximum probability map of Freesurfer parcellations from a group of 75 subjects, affinely aligned to the N27 template. There are a few options:
1. Move the Desai TT_N27 atlas to MNI space. While the transformation from the TT_N27 space to MNI_N27 is exact b
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Daniel Glen
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AFNI Message Board
It looks like it's not reading that dataset at all. That might mean the OS can't find it because it hasn't finished being written yet. Consider adding a small delay before this 3dcopy command. Another approach is to make the reading and writing faster. pigz is the parallelized version of gzip that might help. AFNI format and NIFTI format work differently, so an AFNI format solution
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Daniel Glen
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AFNI Message Board
That is only a warning to let you know that you are dealing with an oblique dataset. As the warning indicates, there can be problems mixing data of differing obliquity, and these may not display correctly with differently oblique datasets in the AFNI GUI. If you already know that, then you can safely ignore that warning. There is an environment variable to turn that off, AFNI_NO_OBLIQUE_WARNING,
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Daniel Glen
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AFNI Message Board
I'm not seeing this problem either. What platform - hardware and operating system are you using?
Those labels are the "crosshair labels" that appear usually above the surfaces in suma. You can switch the default coloring from a white font with black shadows to a black font with white shadows with the F6 key to switch the background color. You can also change the font with this s
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Daniel Glen
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AFNI Message Board
Regarding the swiss cheese part, that will be problematic possibly for the nonlinear alignment. You might start with just an affine alignment to a template to start, where I would expect the "holiness" of the cerebellum not to have a big enough influence on the optimum, single affine matrix transformation for the whole volume. Another approach is to limit the nonlinear alignment to just
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Daniel Glen
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AFNI Message Board
3dBrickStat can take a mask dataset or a non-zero option. Also consider 3dmaskave for a single mask and 3dROIstats for a multi-valued ROI mask dataset like an atlas to apply against your dataset.
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Daniel Glen
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AFNI Message Board
EDIT: Paul beat me to this, but just in case there's a bit of extra useful information, I'll leave this here.
Overlap can be computed with the @DiceMetric or 3dABOverlap programs.
Simple masks can be created with 3dcalc like this way from example 3 in its help:
3. Create a simple mask that consists only of values in sub-brick #0
that are greater than 3.14159:
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Daniel Glen
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AFNI Message Board
Hmm, try copying the dataset first to a temporary dataset to use as a template, outside of Matlab, with "3dcopy mydset+tlrc mycopy". Remove the history of the copy there with "3drefit -denote mycopy+tlrc". Then try the Matlab BrikLoad and WriteBrik with the copy. If it still doesn't work, I can take a closer look. PM me for upload instructions.
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Daniel Glen
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AFNI Message Board
Paul has some cool solutions for showing edges in the volume, but you may be interested in showing contours on surface maps as described in this previous post:
https://afni.nimh.nih.gov/afni/community/board/read.php?1,167734,167743#msg-167743
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Daniel Glen
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AFNI Message Board
I would use InstaCorr for most of the same functionality.
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Daniel Glen
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AFNI Message Board
AFNI's format for stimulation times associated with duration use a colon between the time and duration. You can generate these "married" parameters with 1dMarry. afni_proc.py can take married stimulus timing files as input with options for the stim_times_type (see afni_proc.py example 7 for AM1 or AM2 stimulus timing). (3dDeconvolve's help has information on using -stim_times
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Daniel Glen
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AFNI Message Board
One part of this confusion that's Mac specific is the blocking of DYLD variables from one shell to another. The path must be inherited; otherwise, it wouldn't know where to find afni or suma to begin with. This information is for the System Integrity Protection (SIP) that the MacOS introduced in 2015:
"Spawning children processes of processes restricted by System Integrity Pro
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Daniel Glen
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AFNI Message Board
Add the option, '-ainterp NN' , to your command. That will use nearest neighbor interpolation that's appropriate for ROIs.
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Daniel Glen
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AFNI Message Board
I think that should be fine. I just used the Clusterize plugin for this, and that was the command it showed. The 3dClusterize command apparently needs an additional "-1sided RIGHT_TAIL 0". The within_range option is probably better, so you can skip the temp_range dataset produced by 3dcalc.
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Daniel Glen
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AFNI Message Board
Spent some time with this data. This data was pretty "challenging" because it's only about 5 slices of data, low resolution, spatially and temporally noisy, non-uniform enhancements, and shapes are changing throughout. That's plenty of trouble. Mostly, your recipe seemed pretty close to what I thought I was best.
# restrict data to range
3dcalc -a 'RA_B017_ZDS3_GEPI2
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Daniel Glen
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AFNI Message Board
That command uses the sub-brick volume 5, which is the 6th volume because we use a 0-based counting system.
If the data is far off to start, then use -giant_move. You may want to consider premasking the data too. If you're really stuck, I can help take a look.
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Daniel Glen
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AFNI Message Board
I would probably try with align_epi_anat.py which calls 3dAllineate. Datasets are masked and weighted - depending on which is assigned to be the base dataset and which is the source input. You can also do this directly with 3dAllineate. The aea script can apply the affine transformations as "-child_dset1" or "-child_dset2". You can also choose a -rigid_body alignment if you th
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Daniel Glen
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AFNI Message Board
You can try masking the data explicitly to save only that part of the data. If needed, you can apply the transformation to the pre-masked data.
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Daniel Glen
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AFNI Message Board
3dTcorr1D computes the correlation of a 1D time series with a 3D+time dataset.
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Daniel Glen
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AFNI Message Board
Not sure what you mean by manual way, but there are options you can add to various alignment programs. The -tlrc_opts option controls some of these options. The options depend on what kinds of issues there are in the data. For example, skullstripping may be a problem there that can depend on the anatomy of the subject and the scan. Consider using @SSwarper for both skullstripping and alignment of
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Daniel Glen
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AFNI Message Board
There are several atlases available with subthalamic structures.
Keuken atlas with 3 age ranges (included here with our modal smoothing optionally):
Pauli atlas
More complicated ways -
THOMAS atlas (must install git-lfs package for download and then several packages to generate parcellations)
A version for Parkinson Disease subjects:
Vinod Kumar made this available
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Daniel Glen
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AFNI Message Board
It's hard to tell with only the script. The skullstripping may be part of the problem you're running into, or your anatomical data may have artifacts that limit the alignment. A couple recommendations:
1. Template - use one of the more modern templates instead like the MNI_2009c template. We provide a unifized version you can use with @SSwarper. That program will do the skull strippi
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Daniel Glen
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AFNI Message Board
Just to add to Paul's advice, the BN_Atlas_246_1mm.nii.gz should be in your binary directory (probably ~/abin). I don't know where the other uncompressed one comes from (without the .nii.gz). You may want to fetch that atlas again or even the whole binary package.
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Daniel Glen
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AFNI Message Board
Hi Prantik,
Thanks for letting us know about this issue. We (Rick) are (is) looking into this. It seems to be related to a recent update in Monterey, and the homebrew libraries have not been updated to match.
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Daniel Glen
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AFNI Message Board
Just adding on to Paul's comment, we did find the ventilator and related equipment can affect the BOLD signal.
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Daniel Glen
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AFNI Message Board
You can attach statistical parameters to a subbrick volume with 3drefit -substatpar. These are the parameters from the help:
-substatpar n type v ...
Attach to sub-brick #n the statistical type and
the auxiliary parameters given by values 'v ...',
where 'type' is one of the following:
Stat Types: ~2~
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Daniel Glen
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AFNI Message Board
The sh shell is used by default in Matlab. I tend to use the system() command instead of unix(), but I don't think that will be critical here. Take a look at this previous post to see if the Matlab specific environment variables help.
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Daniel Glen
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AFNI Message Board