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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 Paul,
First off thank you for your help and quick response. I added the -oob_value flag and it worked!
Just a little context to answer your questions, although it is not all that interesting/relevant to anybody except me lol. The script I used wasn't from proc.py. This is a relatively old data set with 2 days of scanning, day 1 was analyzed in surface but day 2 wasn't. So I ap
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naailk90
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AFNI Message Board
Hello everyone,
I am having a little bit of trouble with running a simple group analysis using surface data. I used 3dVol2Surf to map the volume data to the std 141 surface and 2 of my participants do not have the expected number of vertices (198812). I am attaching a screenshot of the 3dinfo if it is of any help.
Thank you
Naail
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naailk90
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AFNI Message Board
Both of the posted solutions worked. Thank you for your help
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naailk90
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AFNI Message Board
Hello everyone,
I am trying to take a previously defined ROI and split it into 3 even sub-divisions along the anterior-posterior axis. Splitting the ROI in half is straightforward with 3dCM but I am having trouble figuring out how I could divide it into thirds.
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naailk90
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AFNI Message Board
Hi everyone,
After trying a million things I was finally able to resolve this issue although I am not sure if it is the best solution long term. The system I am using has a 3090 GPU installed. At some point, I started using nvidia 515 proprietary drivers and that seems to be what's causing the issue. I switched to the open source drivers and the suma GUI works as normal. In hindsight, I pr
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naailk90
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AFNI Message Board
Thank you for the information. Sorry for the slow response, I picked up a pretty bad cold for the last few days (luckily not covid).and have been a little out of it. I am running afni on ubuntu 20.04. What is really weird is when I change the background colour to white, the crosshair labels also become white. I have tried changing the fonts in .sumarc but no luck. I will try installing X11 fonts
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naailk90
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AFNI Message Board
Hi everyone,
I am suddenly having a strange problem with SUMA. The crosshair labels are now the same colour as the background. I tried to change the background colour to white but the label colour also changed to white. I couldn't find anything in .sumarc file that could be related to the label colour. I included screenshots to illustrate the issue. Any help would be appreciated.
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naailk90
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AFNI Message Board
Hi everyone,
I am having a little bit of trouble with converting brik+head format files to a analyze format. I have study specific MNI template in brik and head format when I convert it to anazlyse format with 3dAFNItoANALYZE the axes values change as if it is in a different space now. Now if I take analyze version of the same template and us 3dCopy or 3dCalc to convert back to brik and head i
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naailk90
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AFNI Message Board
Hello everyone,
I am trying to align my anatomical to my functional however I am getting very poor results for some participants (see attached images). After alignment the anatomical looks very wonky and this was happening on quite a few participants. I have tried using different cost functions such as lpa and nmi but have had no luck. When I try the alignment on another computer with an older
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naailk90
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AFNI Message Board
Hello everyone,
I am trying to run a clustersim on surface data but I'm not sure if I am correctly selecting blur values. I know that with 3dclustsim I need to obtain estimates for the noise smoothness. I'm not sure if thats what I am supposed to be doing slow_surface_clustsim.py or if the blur value should be the same as my smoothing kernel. Here is the command I used to test things
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naailk90
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AFNI Message Board
Yes I was working with the user account. I have never had any issues installing afni on a system till this one, it was a very strange problem.
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naailk90
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AFNI Message Board
Hi Rick,
I have been banging my head at this problem today and I was finally able to install AFNI. I became a bit desperate and thought maybe the permissions on the tgz file were incorrect so I changed the permissions on the file (good old chmod 777) and afni was installed. I'm not sure why the permissions on the tgz package had to be changed, it may be some sort security setting my coll
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naailk90
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AFNI Message Board
I have attached the full output of what I ran before and also the output of ls -l ~/abin/.tmp.install.
The .tgz file looks like it is complete and nothing wrong with it.
For which tar the output is /usr/bin/tar
For tar --version the output is bsdrar 2.8.3 - libarchive 2.8.3
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naailk90
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AFNI Message Board
Hi Rick,
Thanks for the quick response. The system is 10.13.6 High Sierra, the system is a Macbook Air.
The command you gave crashed with the same error.
I have tried the following commands:
tcsh @updates.afni.binaries -defaults -package macos_10.12_local
tcsh @updates.afni.binaries -defaults -local_package macos_10.12_local (with package downloaded on the computer)
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naailk90
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AFNI Message Board
Hello everyone,
I am trying to install afni on a colleague's mac computer however the installation keeps failing giving a failure to extract the install package (see attached image). I have tried the app install as well and that failed too. Any help would be appreciated.
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naailk90
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AFNI Message Board
Hi Daniel,
Thanks to your help I was able to get this working yesterday. I appreciate your help!
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naailk90
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AFNI Message Board
I'm still having trouble with this, if anyone can help I would greatly appreciate it
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naailk90
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AFNI Message Board
Hello everyone,
I am trying to create a cmap that will allow me to colour in a ROI overlap image in surface. I was able to set unique values to all three ROIs as well as all possible combinations of overlap. I would like to set a colour scale where a value of 1 is red, 2 is blue, etc etc. I tried using MakeColorMap but have had no luck so far. Any help would be much appreciated.
Naail
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naailk90
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AFNI Message Board
Hello fellow AFNI users,
I have localized a node in the original native mesh and I would like to find the node value of the corresponding anatomical location in the 141 standard mesh. Is there a command to do this in surface?
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naailk90
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AFNI Message Board
Hi Rick,
I realize that you are exactly right and my approach was wrong. By calculating the FDR curves after thresholding I was biasing the results and obtaining odd q values. Thank you for the timely responses.
Naail
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naailk90
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AFNI Message Board
Hi Rick,
Thank you for the response.
As pertinent to the research question I had to remove voxels the showed deactivations in any of the the conditions. That leaves me a total of 31653 nodes (from 3dBrickStats) which significantly reduced from the original 3dDeconvolve results (8176252). Based on what you have said, it seems the voxel count is the reason for the FDR results.
Naail
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naailk90
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AFNI Message Board
Hello everyone,
After conducting a single subject analysis with surface data using 3dDeconvolve I found that the p and q values were very similar. I then used 3dcalc to create new contrasts based on the 3dDeconvolve results and recalculated the FDR curves with 3drefit. To my surprise I found that the corrected q values were now smaller than p. I am aware that this is theoretically possible wi
by
naailk90
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AFNI Message Board
Hello,
I am new to afni so this may be a very simple.
I have a list of coordinates that I have found in native space. I would like to transform those coordinates to tlrc. I have the appropriate epi in both native and tlrc. I know I can use the afni gui to automatically jump to the appropriate coordinates in tlrc when switching from native but I would like to a create script to do this. Woul
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naailk90
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AFNI Message Board