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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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Hi! Just checking in again -- any thoughts on this problem?
Thanks.
by
witherscp
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AFNI Message Board
Hi!
I have downloaded the brainnetome atlas BN_Atlas_246_1mm.nii.gz to use as the parcellation for my DTI processing. How can I convert this NIFTI parcellation into subject DTI space? Previously, I have used fat_proc_map_dti to bring FreeSurfer outputs into DTI space, but this .nii.gz file is not a FreeSurfer output and it is not in the subject's space already, so I don't know how fa
by
witherscp
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AFNI Message Board
Hi,
I tried using dcm2niix_afni to convert my GE DTI blip up / blip down dicom data to NIFTI format. In doing so, I realized that the .bval files that were created did not seem accurate. Every shell had the maximum bval of 1100 except for the first one, which was zero. I think this may be due to a problem with the GE Dicom headers. I found that a previous user in my group extracted the informa
by
witherscp
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AFNI Message Board
Hi,
I have collected a T1w MRI scan using two different scanners for the same patient. In one of these scans, the patient has LPA, RPA, and Nasion fiducials which I have labeled using the "Edit Tagset" Plugin. I want to find the coordinates of these fiducials in the other MRI image where the patient does not have markers on their head. Since I have hundreds of patients like this, I w
by
witherscp
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AFNI Message Board
I get this error when running my group's fMRI processing pipeline:
3ddot -dodice full_mask.p249+orig mask_anat.p249+orig
tee out.mask_ae_dice.txt
dyld: Library not loaded: /sw/lib/libjpeg.9.dylib
Referenced from: /Users/witherscp/abin/3ddot
Reason: image not found
Abort
When I run "afni_system_check.py -check_all", this is my output:
-------------------------
by
witherscp
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AFNI Message Board
Thanks for the help! I ended up using "SurfMeasures -func coord_A" to retrieve the coordinates for every node in both hemispheres. Then, I wrote a python script to find all of the Euclidean distances that I needed. I appreciate your responsiveness.
by
witherscp
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AFNI Message Board
Hello,
I want to find the Euclidean distance between a node in one hemisphere and the location of every surface node in both hemispheres.
For example, for node 105 in the left hemisphere, I want to know how far this is from every node in the right hemisphere and left hemisphere of the pial surface. I am using this command:
SurfDist -I std.141.${hemisphere}.pial.gii -from_node 105L -input
by
witherscp
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AFNI Message Board
Hello,
I created resection masks in volumetric space and transformed them to surface-space on the std.141 mesh using 3dVol2Surf. Before using 3dVol2Surf, I also applied 3dmask_tool with the -fill_holes flag and -dilate_result 2. Most of my masks look really good but they are not perfect, which is totally expected.This is not AFNI or SUMA's fault; it is actually my own human error in valid
by
witherscp
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AFNI Message Board
Thanks for your help! I used method #4 to undump each electrode into a separate file.
by
witherscp
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AFNI Message Board
Hello!
I am using 3dUndump to create 1.5mm radius spheres that correspond to intracranial EEG electrode locations. The problem I am encountering is that multiple electrodes are within very close vicinity to one another, and this is resulting in the voxel value of one electrode overwriting the voxel value of another electrode. How can I make sure that every voxel is preserved? Obviously, it wou
by
witherscp
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AFNI Message Board
Hello,
I am currently using SurfDist to solve a problem that involves the geodesic distance between node pairs on the surface mesh. I know this is a computationally expensive process, especially if I am calculating the distances between many pairs of nodes. Perhaps, you can provide me with some insight on how to approach this problem using the fastest method. Here is what I would like to do:
by
witherscp
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AFNI Message Board
Thanks for the suggestion! Here is the code I ended up using:
# base name for Schaefer parcellation
bn="indt_std.141.${hemi}.Schaefer2018_${num_parc}Parcels_${num_network}Networks"
# iterate over both hemispheres
for hemi in 'rh' 'lh'; do
# get hemi cerebral WM parcel from aparc.a2009s+aseg parcellation
by
witherscp
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AFNI Message Board
Below I have included the code that I am using to convert the niml.dset data (in dt space) to the volumetric space and then convert it to ROIs using 3dROI maker. My plan is to do this for both hemispheres and then merge those hemispheres together using 3dcalc. However, since 3dROImaker inflates each hemisphere by 3 voxels up to the regions with FA>0.2, the ROIs inflate across the midline and o
by
witherscp
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AFNI Message Board
Do I use the std mesh surfaces that are in the "surfatlas" folder or the "surfsets" folder?
To make sure I understand, since these files are already on the standard mesh, I do not need to modify them before visualizing them directly on each subject's FreeSurfer surfaces. These surfaces should look slightly different for each subject on SUMA because their cortical gyri
by
witherscp
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AFNI Message Board
I am using the Schaefer 400 parcels (17 networks) atlas as my ROIs for tractography using 3DTrackID. Here is my current workflow:
mri_surf2surf --> resample Schaefer parcellation from fsaverage subject onto subject of interest
FSread_annot --> convert annot file to Suma-usable niml.dset format
SurfToSurf --> register niml.dset from original surface onto standard mesh of linear d
by
witherscp
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AFNI Message Board
I also tried running the command
$DYLD_LIBRARY_PATH
in my terminal, and I got this output:
-bash: /opt/X11/lib/flat_namespace:/opt/X11/lib/flat_namespace: No such file or directory
But I am unsure why it says no such file or directory because I am able to navigate to this directory using
cd /opt/X11/lib/flat_namespace
by
witherscp
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AFNI Message Board
I reinstalled R and installation of the R packages necessary for AFNI. This is the new output, when I check to see whether AFNI is working properly. I am still getting the same error, but it shows that my R version is 3.6.2. Any other suggestions?
-------------------------------- general ---------------------------------
architecture: 64bit
system: Darwin
release:
by
witherscp
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AFNI Message Board
I am not sure how to resolve the fixes that I need to make. How do I set the DYLD_LIBRARY_PATH? Also, how can I resolve the issue involved with 3dMVM? Thanks for the help!
-------------------------------- general ---------------------------------
architecture: 64bit
system: Darwin
release: 19.6.0
version: Darwin Kernel Version 19.6.0: Th
by
witherscp
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AFNI Message Board