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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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Pages: 12
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Hi team, is there a recommended pipeline for preparing a multi-voxel pattern analysis of a task? I searched the afni_proc.py help page but didn't find resources there. I found this resource for an afni pipeline but wanted to ask here, too.
Thank you!
Josh
by
jgowin
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AFNI Message Board
Converting back to WSL1 solved our problem and we were able to use the AFNI GUI. Thanks for the support!
by
jgowin
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AFNI Message Board
Daniel, thanks!
We are still having trouble resolving the issue in WSL2 but I appreciate the link to the other thread. It was useful to know that this problem has been encountered before. We are going to try to convert back to WSL1 and see if that resolves it. Otherwise, we will explore the links you shared in the other post to some forums where other people have encountered this.
I'll k
by
jgowin
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AFNI Message Board
Thanks Rick. We are trying to get things installed on a local machine for now so we aren't using ssh. I am perplexed. We are in a Windows machine and using Ubuntu. We had initially used Ubuntu version 20.04 and then we removed that and now we're trying Ubuntu 18.04 but we are getting the same error.
by
jgowin
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AFNI Message Board
Hi Paul, We are on a Windows machine using Ubuntu. Here's the output
kirkprok@RAD-D-BBZVHL2:~$ afni_system_check.py -check_all
-------------------------------- general ---------------------------------
architecture: 64bit
system: Linux
release: 5.10.16.3-microsoft-standard-WSL2
version: #1 SMP Fri Apr 2 22:23:49 UTC 2021
distribution
by
jgowin
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AFNI Message Board
Hi team,
We are trying to set up a new installation and I encountered an error I haven't seen before. Can you help me resolve this:
Precompiled binary linux_ubuntu_16_64: Sep 1 2021 (Version AFNI_21.2.06 'Nerva')
** Version check disabled: AFNI_VERSION_CHECK forbids
Thanks go to KM Donahue for useful feedback
Initializing: X11Error: Can't open display: :0.0
by
jgowin
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AFNI Message Board
Thanks, Rick! That's a helpful example. Just to be sure I understand, in the example it looks like the seed timeseries comes from the .errts file, not from the pb04 scaled timeseries (it's usually pb04 for me, but could be another value for others :) . Is that correct?
by
jgowin
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AFNI Message Board
To follow up on my own message, I found the following:
-write_ppi_3dD_scripts : flag: write 3dD scripts for PPI analysis
e.g. -write_ppi_3dD_scripts \
-regress_ppi_stim_files PPI_*.1D some_seed.1D \
-regress_ppi_stim_labels PPI_A PPI_B PPI_C seed
This seems like a useful pathway for me to follow (altho
by
jgowin
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AFNI Message Board
Hi, forgive me if I have done a poor job searching, but I couldn't find an example of using afni_proc for a connectivity analysis during a task. I think at one point I had tried conducting a complete task analysis and then using the .errt output from 3dDeconvolve. Then I extracted the timecourse of a seed and conducted a second 3dDeconvolve using the timecourse as the regressor. Is something
by
jgowin
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AFNI Message Board
I just saw this in my output.proc file:
auto_warp.py -base MNI_avg152T1+tlrc -input 0322201401_ns+orig -skull_strip_input no
#++ auto_warp.py version: 0.03
-- clearing AFNI_COMPRESSOR ...
Do I need to prevent auto_warp.py from clearing my AFNI_COMPRESSOR setting?
by
jgowin
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AFNI Message Board
I updated the files and now here is what I get.
$ grep AFNI_COMPRESSOR ~/.afnirc ~/.cshrc ~/.bash*
/home/jgowin/.afnirc:AFNI_COMPRESSOR = NONE
/home/jgowin/.cshrc:setenv AFNI_COMPRESSOR NONE
/home/jgowin/.bashrc:AFNI_COMPRESSOR=NONE
/home/jgowin/.bashrc:export AFNI_COMPRESSOR
Now, most of my files are saving uncompressed as .BRIK files. However, at the @auto_tlrc stage, it is still sav
by
jgowin
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AFNI Message Board
Here's the output.
$ grep AFNI_COMPRESSOR ~/.afnirc ~/.cshrc ~/.bash*
/home/jgowin/.afnirc:unset AFNI_COMPRESSOR
grep: /home/jgowin/.cshrc: No such file or directory
/home/jgowin/.bash_history:AFNI_COMPRESSOR
/home/jgowin/.bash_history:unset AFNI_COMPRESSOR
/home/jgowin/.bash_history:unsetenv AFNI_COMPRESSOR
/home/jgowin/.bashrc:unset AFNI_COMPRESSOR
/home/jgowin/.bashrc~:unset AF
by
jgowin
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AFNI Message Board
The default shell is bash but I run the proc.SUBJ script using the suggested tcsh proc.SUBJ -xef
I may have to contact the root user to change the local environment. Thanks for helping me get to the bottom of this.
by
jgowin
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AFNI Message Board
I have tried including "unsetenv AFNI_COMPRESSOR" at the start of the proc.SUBJ script but it hasn't prevented the files to be compressed as .gz. Is there another way to unset the AFNI_COMPRESSOR variable?
Thanks!
by
jgowin
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AFNI Message Board
Yes, it looks like the .gz file is there:
$ ls -l awpy/base.*
-rw-rw----+ 1 jgowin paulus-lab 315649 Aug 23 18:07 awpy/base.nii.gz
How do I disable the compressor, or work around it?
by
jgowin
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AFNI Message Board
I created a proc.subj script using afni_proc.py and did not see any errors during the creation of the script. However, when trying to run the script, I run into problems during the transformation. It seems like it is not recognizing base.nii but I cannot understand why not. Does the following give you any ideas why not?
++ 3dUnifize: AFNI version=AFNI_16.2.16 (Sep 4 2016) [64-bit]
+ Pre-pr
by
jgowin
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AFNI Message Board
HUMAN PSYCHOPHARMACOLOGY
NATIONAL INSTITUTE ON ALCOHOL ABUSE AND ALCOHOLISM, BETHESDA, MD AND SURROUNDING AREA
Position Description:
We are recruiting a postdoctoral fellow to conduct research in the Section on Human Psychopharmacology in the intramural program of the National Institute on Alcohol Abuse and Alcoholism (NIAAA), one of the National Institutes of Health (NIH), Department of H
by
jgowin
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AFNI Message Board
I was trying to play with ETAC today. I ran a two group 3dTtest++ with -ETAC on seed-based resting state data. I had done the preprocessing with a 6mm blur so I didn't use the -ETAC_blur option.
For the results output, I am unclear if I should set the threshold bar to 0.05 or if I should set the threshold bar to a lower value, like 0.002.
For example, how should I interpret a "sig
by
jgowin
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AFNI Message Board
Hi Rick,
Here's the matrix you requested:
qto_xyz 400 16 -3.75 -0.0 -0.0 123.535103 0.0 3.75 -0.0 -113.441299 -0.0 0.0 3.8 -62.141651 0.0 0.0 0.0 1.0
sto_xyz 656 16 -3.737319 -0.086822 -0.29959 121.573715 -0.269864 2.658937 2.665612 -114.062431 -0.148725 -2.642918 2.691609 42.776073 0.0 0.0 0.0 1.0
The file was created by a transformati
by
jgowin
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AFNI Message Board
num_fields = 43
all fields:
name offset nvals values
------------------- ------ ----- ------
sizeof_hdr 0 1 348
data_type 4 10
db_name 14 18
extents 32 1 0
session_error 36 1 0
regular 38 1 r
dim_info 39 1
by
jgowin
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AFNI Message Board
$ 3dinfo -av_space -space -prefix nv_3537997_20141103_resting_state.nii
+tlrc ORIG nv_3537997_20141103_resting_state.nii
$ 3dinfo -av_space -space -prefix nv_3537997_20141103_resting_state+orig
+orig ORIG nv_3537997_20141103_resting_state
I see that the NIFTI file has +tlrc. What should I do about that?
by
jgowin
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AFNI Message Board
If this helps, here is the output of 3dinfo for the NIFTI file and for the 3dcopied file in orig space (the one that is grossly misaligned)
$ 3dinfo nv_3537997_20141103_resting_state.nii
++ 3dinfo: AFNI version=AFNI_17.2.10 (Aug 30 2017) [64-bit]
Dataset File: nv_3537997_20141103_resting_state.nii
Identifier Code: XYZ_Kjr2NHWk-5QN8JmicU5DOw Creation Date: Fri Nov 21 09:39:47 2014
Temp
by
jgowin
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AFNI Message Board
Hi,
I am trying to convert epi NIFTI files to BRIK format, but am having problems. When I do 3dinfo on the NIFTI files, it says that they are in orig space. When I use 3dcopy to convert to BRIK (3dcopy inset prefix) the output is in tlrc space. When I try to use 3drefit to change the view back to orig, the image moves dramatically and no longer aligns with my anatomical. Is there a reason w
by
jgowin
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AFNI Message Board
You're right, that's where the problem originated. I'll see if I can resolve it. Thank you.
by
jgowin
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AFNI Message Board
The attached image shows the problem (the values are all at the top of the image) but I don't know where this may have gone wrong.
by
jgowin
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AFNI Message Board
As a follow up, I looked at the following:
$ 3dmaskave -mask follow_ROI_FSWe+tlrc rm.det_pcin_rall+tlrc
++ 3dmaskave: AFNI version=AFNI_17.2.10 (Aug 30 2017) [64-bit]
+++ 9353 voxels survive the mask
0.237365 [9353 voxels]
0.070627 [9353 voxels]
-0.0387127 [9353 voxels]
0.025132 [9353 voxels]
0.125903 [9353 voxels]
etc
So the 0 values are only showing up in the FSvent mask, but I s
by
jgowin
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AFNI Message Board
Hi Rick,
Here's the output:
$ 3dmaskave -mask follow_ROI_FSvent+tlrc rm.det_pcin_rall+tlrc
++ 3dmaskave: AFNI version=AFNI_17.2.10 (Aug 30 2017) [64-bit]
+++ 306 voxels survive the mask
0 [306 voxels]
0 [306 voxels]
0 [306 voxels]
0 [306 voxels]
0 [306 voxels]
0 [306 voxels]
0 [306 voxels]
etc...
I don't understand why those values would be 0
by
jgowin
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AFNI Message Board
Hi,
I encountered the following error with several participants today when their proc scripts reached 3dpc. I haven't seen it before so I don't know what needs to be fixed. Any ideas?
Error: 3dpc -mask follow_ROI_FSvent+tlrc -pcsave 3 -prefix rm.ROIPC.FSvent rm.det_pcin_rall+tlrc
++ 3dpc: AFNI version=AFNI_17.2.09 (Aug 22 2017) [64-bit]
** ERROR: covariance diagonal (1,1) =
by
jgowin
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AFNI Message Board
Hi, I am conducting a resting state functional connectivity analysis and I am about to use 3dTcorr1d to correlate a seed's signal with the rest of the brain. Is there any information available for how choosing -pearson vs -spearman, -ktaub or -quadrant would affect my results?
I'd appreciate any insight!
Josh
by
jgowin
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AFNI Message Board
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