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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:
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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
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I am running a searchlight RSA analysis.
1) I use 3dmaskdump to get the coordinates of every voxel in the brain mask. My understanding is that this outputs the coordinates in RAI orientation.
3dmaskdump -overwrite -mask /Users/lynna3/Documents/Projects/EF_Math/ref/mask/BN_atlas_group_HaskinsPeds_2.5_mask_RAI+tlrc.HEAD \
-noijk -xyz \
-o /Users/lynna3/Documents/Projects/EF_Math/Processed_D
by
aclynn11
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AFNI Message Board
Thanks Daniel,
I've worked out the RAI specific issue. I've make sure that the 3dmaskdump to 3dUndump pipeline is consistently in RAI, which I then 3dresample to LPI to match the original data orientation. When putting together this analysis pipeline I worked with the ijk system but I found keeping things in RAI was easier.
Moreover, the group data set is aligned with the HaskinsP
by
aclynn11
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AFNI Message Board
adding the following code to the startup script fixed the problem:
pydir = '/Users/andrewlynn/miniconda3/bin';
setenv('PATH',)
I'm now troubleshooting a different issue..
Thanks for your help!
by
aclynn11
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AFNI Message Board
yes, I have python installed via miniconda3
-------------------------------- general ---------------------------------
architecture: 64bit
system: Darwin
release: 21.4.0
version: Darwin Kernel Version 21.4.0: Mon Feb 21 20:34:37 PST 2022; root:xnu-8020.101.4~2/RELEASE_X86_64
distribution: 10.16
number of CPUs: 6
apparent
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aclynn11
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AFNI Message Board
Thanks for the quick reply.
Other AFNI scripts work. I run the following code to make sure AFNI and MATLAB are working together:
setenv('DYLD_FALLBACK_LIBRARY_PATH',[ '/Users/conradbn/abin:' getenv('DYLD_FALLBACK_LIBRARY_PATH') ])
% is the path to AFNI already set?
= unix('3dcopy');
% if not, then we will look for it...
if afninotfound
%
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aclynn11
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AFNI Message Board
Hi all,
we run most of our processing pipeline through MATLAB for several reasons, but a recent update to MATLAB has introduced an issue with the afni python scrips (e.g., 1d_tool.py).
for example,
unix(['1d_tool.py -help')
returns
env: python: No such file or directory
ans =
127
but, when run in zsh, the expected help text is returned.
I know this is
by
aclynn11
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AFNI Message Board
I've also reoriented the HaskinsPeds-Freesurfer anatomical file to LPI so it matches the dataset, but this does not fix the problem.
by
aclynn11
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AFNI Message Board
through 3dUndump
----- HISTORY -----
{AFNI_21.3.10:macos_10.12_local} 3dUndump -xyz -datum float -prefix /Volumes/NBL_Projects/NBL_WorkingPapers/HomeMath_RSA/groupanalyses/ROI/Group_within_ratio_Region_digitratio_t_RAI -master /Volumes/NBL_Projects/NBL_WorkingPapers/HomeMath_RSA/ref/atlas/BN_atlas_group_HaskinsPeds_2.5_mask_RAI+tlrc.HEAD /Volumes/NBL_Projects/NBL_WorkingPapers/HomeMath_RSA/g
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aclynn11
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AFNI Message Board
Perhaps that's part of the issue. The group dataset I'm trying to visualize seems misaligned to the HaskinsPeds T1.nii and *.spec file. Maybe the group data needs to be regrided?
I'm visualizing using AFNI+SUMA:
afni -niml &
suma -spec ../../ref/HaskinsPeds/freesurfer/HaskinPeds/SUMA/std.141.HaskinPeds_both.spec -sv ../../ref/HaskinsPeds/freesurfer/HaskinPeds/SUMA/T1_new
by
aclynn11
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AFNI Message Board
Thanks Daniel! This helped the "orig to tlrc" issue but the dataset image is misaligned, presumably because the HaskinsPeds.spec file is in freesurfer space.
Is there a standard process for creating the spec files for ref images like the ones that come included in SUMA like MNI152_2009? This way I could create the surface mapping directly on the HaskinsPeds template without going to
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aclynn11
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AFNI Message Board
Hello all,
I'm trying to project a volume onto the surface using the AFNI+SUMA interface. The data are in HaskinsPed space, however I can't seem to get the right parcellation to pass to SUMA so that the group map is aligned with the template.
My attempt was to run the HaskinsPed template through freesurfer then use @SUMA_Make_Spec_FS to make the spec file. This step was successfu
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aclynn11
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AFNI Message Board
in debugging I can re run the command after it crashes and then it runs.
by
aclynn11
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AFNI Message Board
Hello everyone,
I am running a search light analysis which has successfully completed with a radius of 14. I am now attempting to run at a larger radius = 28 and am running into a fatal error when some (not all) voxels are the center. I thought it might be due to the xball being drawn near a boundary, but that doesn't seem to be the case.
This is the code I pass in which I loop through
by
aclynn11
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AFNI Message Board
I am working on a searchlight analysis and am using 3dmaskdump and 3dUndump in MATLAB. However, after running the searchlight, the results seem to be flipped in orientation -- even though the 3dinfo -verb output says all data are in LPI.
For example, I get a series out errors like this:
[7m*+ WARNING:[0m File /Users/andrewlynn/Desktop/sf_afni_tmp/test.txt line 452016: y coord=-92.5 is
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aclynn11
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AFNI Message Board
thank you all! This would then apply to 2.5mm3 voxels, too?
Andrew
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aclynn11
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AFNI Message Board
Could someone confirm that the "-xball x y z r" option for 3dmaskdump specifies radius in mm?
Andrew
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aclynn11
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AFNI Message Board
Of course, now that I have tried one more thing it seems to have worked.. I simply opted the orig/ & orig.mgz from the ${fsdir}/freesurfer/fsaverage/ directory and the script proceeded.
Thanks again for your help!
by
aclynn11
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AFNI Message Board
Thanks for your help! I'm just picking this back up and am still struggling.
It looks like the Brainnetome fsaverage isn't a full recon-all and is missing orig/orig.mgz. So @SUMA_Make_Spec_FS errors.
***************************************************************
++ Running @SUMA_Make_Spec_FS version: 2.2.4
++ will track 1 extra annot labels
failure: cannot find directory
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aclynn11
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AFNI Message Board
Thanks so much! There is a surface version of the Brainnetome mapped to fsaverage. Would that route be cleaner?
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aclynn11
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AFNI Message Board
Hello all,
I am trying to convert the Brainnetome surface atlas which is in a 164k mesh and Gifti format to the 36k niml.dset format common to AFNI. I am new to surface analyses and find the multiple file formats confusing. My initial attempt was to use SurfToSurf, but this output a 1D file without node ROI value and a niml.M2M file which I wasn't expecting.
Could you please advise on
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aclynn11
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AFNI Message Board
Hello everyone,
I am searching for a Brainnetome atlas in surface space (ideally AFNI's 36K nodes). Has this already been created?
Andrew
by
aclynn11
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AFNI Message Board
Thanks for your response Daniel. I, too, am confused. I am using an atlas of visual cortical regions (Wang et al 2015, Cerebral Cortex) where each regions is assigned one integer value. I am hoping to obtain the center mass for each visual cortical ROI. I had to use CONN toolbox, which required me to import an *.annot file to use the atlas. CONN toolbox then output a *.nii file. Since I'm mo
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aclynn11
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AFNI Message Board
Hello,
I am familiar with afni's volume-based tools, but I have no shifted toward using surface-based tools from freesurfer and CONN toolbox. In order to upload an visual cortex atlas consisting of 50 ROIs I first converted it to a .nii file. I'd now like to determine the coordinates of each ROI center of mass. For a volume-based data set I would use something like 3dClust. However,
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aclynn11
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AFNI Message Board
Has anyone had issues with using AFNI on macOS 10.14? I am considering updating but don't want to break anything.
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aclynn11
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AFNI Message Board
I see that 3dDeconvolve is an OLSQ regression and 3dREMLfit is a GLSQ. I was under the assumption that 3dDeconvolve handled autocorrelation of the time series since this seems to be important in fMRI data. Is this true, or is 3dREMLfit the only program that does so? If this 3dREMLfit is the only program, then in what instances would one use 3dDeconvolve? Shouldn't all fMRI data be handled wi
by
aclynn11
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AFNI Message Board
Thank you Rick!
So to clarify, scaling should be done before nuisance regression. I should not then assume that if NO SCALING is done that the errts output is comparable across subjects.
Best,
Andrew
by
aclynn11
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AFNI Message Board
Hmm, it's weird. The export has been added to my ~/.bashrc profile, multiple time now, in fact (see below). However, each time I open a new terminal and open afni it seem i need to export DYLD_LIBRARY_PATH=/opt/X11/lib/flat_namespace on the command line.
Sorry for being a bit naive here. I thought once added to my bash profile that it would run that each time I open a new window and there
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aclynn11
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AFNI Message Board
Hi all,
Forgive me for a potentially naive question. I am preprocessing multiple runs that should be scaled so they are comparable across subjects and runs. Per convention, percent signal change will do. I've run all of the steps, slice time correction, deobliquing, and motion correction. I think input this time series into 3dDeconvolve to regress out motion parameters, as well as CSF and
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aclynn11
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AFNI Message Board
echo $DYLD_LIBRARY_PATH is blank.
Looks like i need to reset this path according to the output txt below.
-------------------------------- general ---------------------------------
architecture: 64bit
system: Darwin
release: 16.7.0
version: Darwin Kernel Version 16.7.0: Thu Jun 15 17:36:27 PDT 2017; root:xnu-3789.70.16~2/RELEASE_X86_64
dis
by
aclynn11
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AFNI Message Board
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