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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
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Hi,
I want to map certain x y z values to a brain region. Most of them are in Thalamus. So I would like to use an atlas that can differentiate between them and not give Thalamus for all of them. Can you recommend which one I should use? I am using the whereami function.
I tried the HCP atlas, but it had no match for a lot of voxels in the thalamus.
Thanks,
Prateek Sasan
by
prateeksasan1
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AFNI Message Board
Hi,
Is it possible to have atlases like aal90 and harvard oxford in the whereami command? I am using that to map my selection voxels to brain areas and it would be great if i could do it for these atlases as well.
Thanks.
Prateek Sasan
by
prateeksasan1
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AFNI Message Board
I am doing an analysis where i end up selecting a subset of brain voxels responsible for a disease. I would like to do further statistical analysis on this subset of voxels. It would be of great help in presenting my results if i can link each voxel with its brain area based on some atlas. That is, lets say i have selected 100 voxels from the brain. Instead of saying that they are voxel 1, voxel
by
prateeksasan1
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AFNI Message Board
Hi,
Thanks. i figured out both of the problems. The 256/257 is a problem with readafni function in R. using 3dbrickstat i get 0 and 1. The other problem i was facing was regarding different results for HEAD and BRIK, that was again due to running with R. In one of them i accidently put the code in 2 lines which introduced a \n operator and that made the difference
Sorry for the confusion.
by
prateeksasan1
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AFNI Message Board
I downloaded afni on windows (wsl) using the steps given on the afni website and i still see 256 and 257. This is the comment i get.
3dmask_tool -input bin_rest_binarized*+orig.HEAD -prefix mask_inter -frac 1.0
++ processing 28 input dataset(s), NN=2...
++ padding all datasets by 0 (for dilations)
++ frac 1 over 28 volumes gives min count 28
++ voxel limits: 238386 clipped, 183 survive
by
prateeksasan1
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AFNI Message Board
Hi,
Thanks for the reply. I deleted the files and ran the code again. Now the result i get using BRIK.gz and HEAD are the same but i still get 256 and 257 as values. Here are the results of codes you told me to run (I am running it on OSC owens server):
afni -ver
Precompiled binary linux_openmp_64: Sep 2 2020 (Version AFNI_20.2.16 'Aulus Vitellius')
ls bin_rest_binarized*
by
prateeksasan1
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AFNI Message Board
Hi,
So i have 28 binarized maps (got using 3dcalc) and i want to find the intersection. I run the following command and have 2 questions regarding it:
3dmask_tool -input bin_rest_binarized*+orig.HEAD -prefix mask_inter \ -frac 1.0"
1. What is the difference between giving the input as bin_rest_binarized*+orig.HEAD and bin_rest_binarized*+orig.BRIK (i get very different intersection
by
prateeksasan1
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AFNI Message Board
I get the following
-------------------------------- general ---------------------------------
architecture: 64bit ELF
system: Linux
release: 3.10.0-1062.18.1.el7.x86_64
version: #1 SMP Wed Feb 12 14:08:31 UTC 2020
distribution: Red Hat Enterprise Linux Server 7.7 Maipo
number of CPUs: 28
apparent login shell: bash
shell R
by
prateeksasan1
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AFNI Message Board
Hi,
This is probably a very basic question. i am new to afni and using my university server. I am trying to run afni on OSC. i dowloaded the .tgz file (linux_openmp_64.tgz) and then unzipped it using tar zxvf linux_openmp_64.tgz. It created a new folder which has all these files, but if i enter the directory and press afni. i get an error. do i have to do something after that? i tried to type
by
prateeksasan1
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AFNI Message Board
I have 18 ROI centers. I use 3dUndump to make 18 ROI masks of radius 10 (giving values 1-18). Because of the large size, there are overlaps. So when i combine them using 3dcalc using formula (a+b+c+d+e+f+g+h+i+j+k+l+m+n+o+p+q+r) and then do 3dNetCorr, i end up with 20 columns with codes 1-18 , 25 and 28. Can you suggest how to deal with this? I would still want 18 ROIs in the end. My guess is
by
prateeksasan1
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AFNI Message Board
Hi,
Sorry for the late reply. I for some reason did not get a mail about this so assumed that noone answered. I am further along my quest but i am struggling with dealing with overlapping ROIs.
I have 18 ROI centers. I use 3dUndump to make 18 ROI masks of radius 10. Because of the large size, there are overlaps. So when i combine them using 3dcalc using formula (a+b+c+d+e+f+g+h+i+j+k+l
by
prateeksasan1
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AFNI Message Board
Hi,
I am new to both AFNI and Ubuntu(on Windows). I want to make 18 ROIs and extract various data on these 18 ROIs like correlation matrix, avergae time series etc.
I tried the following and it didnt work.
I saved a txt file with the xyz coordinates of all 18 roi.'s 1 in each line. I also added a number as a 4th dimension. Then used 3dUndump to make a mask but now when i run 3dNet
by
prateeksasan1
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AFNI Message Board