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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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I solved this! I don't know how to delete the post, but no help needed.
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Ana Navarro Cebrian
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AFNI Message Board
Hi all,
I have a group analysis in the volume and I would like to display it on the surface. I just want to make sure that I understand this. Do I need to work on each individual subject first (map each subject's data to the subject's surface) and then repeat the 3dttest++ for group analysis with the surfaces? Is there another (better) way to visualize my group analysis on a standard
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Ana Navarro Cebrian
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AFNI Message Board
Thanks, Cesar! Changing the censoring threshold to 0.3 helped, as you suggested. I've decided to exclude this subject at the end. Thanks a lot for your message anyway because this is clear to me now.
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Ana Navarro Cebrian
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AFNI Message Board
Hi!
I have a subject with quite a lot of censoring. However, the following afni_proc works well:
afni_proc.py -subj_id sub11 -script proc.sub11 -scr_overwrite -blocks \
despike tshift align tlrc volreg blur mask regress -copy_anat \
/anatomy/sub11.nii -dsets \
/resting_state/sub11_1.nii \
/resting_state/sub11_2.nii \
-tc
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Ana Navarro Cebrian
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AFNI Message Board
Thanks.
My goal is to calculate the functional connectivity of several seeds that are close to each other. Since they are close to each other, there will be a lot of common variance between them and I wanted to just see the unique variance for each of them. I thought I could do that (getting just the unique correlations for each seed) by orthogonalizing each seed's time series with respect
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Ana Navarro Cebrian
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AFNI Message Board
Hello all,
I've been using 3dTcorr1D to calculate a seed's whole brain correlation. Now, I would like to remove the mutual correlations' variance between this seed and another seed correlation (maybe orthogonaling their time-series) and I thought maybe you had any suggestions about how to do this with afni or what function I could use. Sorry for the general question.
Thanks f
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Ana Navarro Cebrian
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AFNI Message Board
Thanks a lot for your reply, Rick. I always learn a lot from these comments.
I followed your suggestions and ended up repeating the preprocessing from scratch using the afni_proc.py commands this time. I followed example 11 and used the FS masks. Everything seemed quite straightforward and the data looks great.
Thanks again!
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Ana Navarro Cebrian
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AFNI Message Board
Thanks for your comment. This clarifies some things.
I imagine you refer to the text file "proc.sub" created by uber_subject.py. Yes, I've checked those files.
I'm taking a look a afni_proc. I will use the output (errts.sub.tproject+tlrc.) from my previous preproc analysis (done with uber_subject) and just run afni_proc to regress WM and ventricles, instead of running ev
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Ana Navarro Cebrian
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AFNI Message Board
Thanks a lot for the message!
Isn't afni_proc.py what's used by uber_subject.py?
I already processed this resting state data using uber_subject.py.
What I'm trying to do now is to regress out ventricles and WM. I was also trying to regress out the entire global signal for comparison.
Can I use ventricles and WM as regressors in afni_proc.py? I couldn't see any option
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Ana Navarro Cebrian
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AFNI Message Board
Hi again,
I've tried -uniformize and -anat_has_skull in case any of these could help with the "could not strip skull" error, but it didn't work.
I understand that the problem could be that the EPI I'm using is the output from the resting state uber_subject. What I don't understand is why this error only happens in half of the subjects.
Any thoughts?
Thanks!
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Ana Navarro Cebrian
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AFNI Message Board
Hi all,
I have resting state data from a group of subjects for whom I run uber_subject.py. Now I'm running afni_restproc.py, using the file errts.sub.tproject+tlrc. that results from uber_subject.py.
The script works for many of my subjects (the majority of them), but there is a problem with some subjects that I don't know how to interpret. Here's the first error message that
by
Ana Navarro Cebrian
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AFNI Message Board
Hi Rick,
Based on your message, I've tried several things (including the -mast_dxyz option in some cases), but nothing worked.
First thing, trying to answer your question: The ROI is in the correct spatial location when overlayed on the anatomical T1 original dataset from freesurfer. Although I'm not sure if that's the anatomical I should be using in -source as you mentioned.
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Ana Navarro Cebrian
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AFNI Message Board
The warp.anat.Xat.1D file was generated when I run uber_subject.py for resting state data. I assumed that that warp.anat.Xat.1D file was the matrix that resulted from the alignment of the tlrc template and the anatomical image, but I don't know for sure.
In any case, I just noticed what could be the main issue: The ROI was created in the same subject that I'm using in afni now, howev
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Ana Navarro Cebrian
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AFNI Message Board
Hi all,
I have a binary ROI in the original space that I had created using freesurfer. Now I'm using 3dallienate to transform it to tlrc space, but I don't get the tlrc ROI in the right location. Here's the line that I'm using:
3dAllineate -prefix stand_ROI -input ROI.nii -master anat_w_skull_warped+tlrc. -1Dmatrix_apply warp.anat.Xat.1D -final NN
I'm guessing that
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Ana Navarro Cebrian
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AFNI Message Board
Hi Gang,
I'd like to calculate resting-state correlations between every voxel of a big region of interest and the rest of the brain to look at how the connectivity of this region changes as you move from anterior to posterior voxels. Instead of looking at the correlations for every single voxel, first, I was going to create clusters based on their correlation ranges. I guess what I need t
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Ana Navarro Cebrian
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AFNI Message Board
Hi all,
I would like to subdivide a region into clusters of voxels with high correlations between them. What's the best approach to do this? Is there an afni function that can help me with this? or do I have to calculate the correlations for each voxel? I was just reviewing 3dClusterize and 3dMerge, but they don't seem helpful for what I need.
Thanks!
Ana
by
Ana Navarro Cebrian
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AFNI Message Board
Dear all,
I'm trying to understand what the y-axis is exactly in these two graphs. I understand that in motion_subj_censor.1D, the TRs with "0" in the y-axis are those that have been censored and removed, is that correct?
Also, I understand that outcount.run.1D shows the number of outliers per TR, but what does a 0.015 value in the y-axis mean, for example?
Thank you for any
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Ana Navarro Cebrian
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AFNI Message Board
Hi all,
I often see in papers that the first two preprocessing steps they use are:
First, compensation of systematic, slice-dependent timeshifts.
Second, elimination of systematic odd-even slice intensity differences caused by interleaved acquisition.
I'm a little confused with the second... Aren't odd-even slice intensity differences caused by slice-dependent timeshifts as well?
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Ana Navarro Cebrian
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AFNI Message Board
Thanks again, Justin.
None of the Digicert have expired.
- I use bash.
- The output of "which curl" is /usr/bin/curl
- I tried to manually download homebrew using the letter k after -fsSL as you suggested and I still get the same SSL certificate problem message.
-So it didn't work. In any case, the output for "brew config" is the following:
HOMEBREW_VERS
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Ana Navarro Cebrian
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AFNI Message Board
Thanks a lot, Justin:
1.
I don't have problems getting in in a browser.
2.
When I try
brew install netpbm
I get the SSL certificate error message:
==> Tapping homebrew/core
Cloning into '/usr/local/Homebrew/Library/Taps/homebrew/homebrew-core'...
fatal: unable to access ';: SSL certificate problem: Untrusted root certificate
Error: Failure while executin
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Ana Navarro Cebrian
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AFNI Message Board
Hi!!
Just an update.. I restarted my computer after my message yesterday and tried the AFNI installer again. Still the same error messages
Any help would be greatly appreciated!
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Ana Navarro Cebrian
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AFNI Message Board
Thank you very much for your response!
brew doctor gives me the following messages:
Warning: "config" scripts exist outside your system or Homebrew directories.
`./configure` scripts often look for *-config scripts to determine if
software packages are installed, and which additional flags to use when
compiling and linking.
Having additional scripts in your path can confuse so
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Ana Navarro Cebrian
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AFNI Message Board
Hi!
I've been trying to install AFNI using the afni_macOS_install_BETA_V2.app but I'm having problems installing netpbm. Please, help! I've tried everything I could possibly try.
I have MacOS El Capitan 10.11.6.
It could be a problem with a certificate, but I have no idea how to solve it.
I also tried to install netpbm not using homebrew, but it doesn't seem to work
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Ana Navarro Cebrian
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AFNI Message Board