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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'm running a 3dANOVA3 with two groups (HVs & patients), with three resting state runs per participant (1,2,3) and looking for an effect over time/runs (presumably fatigue). It's not clear to me from the AFNI help text what the difference is between type 4 and type 5 in the model, and what is meant by "C(A)" for type 5? Here's the help text on the type option:
3dANOV
by
krisknut
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AFNI Message Board
I had to do some cleanup before the yum search would work, based on the advice at , but was then able to install the latest version of the 64 bit libGLU.sl.1.
Many thanks.
by
krisknut
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AFNI Message Board
Typing /usr/lib/libGLU.so.1.3.1 gives:
/usr/lib/libGLU.so.1.3.1: ELF 32-bit LSB shared object, Intel 80386, version 1 (SYSV), dynamically linked, BuildID=1b0e3e1a778c6feed1b251cc8383c60bfce1b012, stripped
by
krisknut
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AFNI Message Board
When trying to install afni on a new Linux computer, afni system check gives me three errors, one each for SUMA, 3dSkullStrip and SurfMesh, however libGLU.so.1 is found in /usr/lib as a link to libGLU.so.1.3.1 as shown here:
cd /usr/lib
ls -l libGLU*
lrwxrwxrwx. 1 root 15 Nov 6 10:34 libGLU.so.1 -> libGLU.so.1.3.1
-rwxr-xr-x. 1 root 560272 Jun 10 2014 libGLU.so.1.3.1
so it's
by
krisknut
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AFNI Message Board
I have a similar problem.
When I run the three suggested commands, I get:
~: R RHOME
/Library/Frameworks/R.framework/Resources
~: ls -l /Library/Frameworks/R.framework/Versions/*/Resources/lib/libR.dylib
-rwxrwxr-x 1 root admin 4071728 Jun 23 19:50 /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib
-rwxrwxr-x 1 root admin 4071728 Jun 23 19:50 /Library/Frameworks
by
krisknut
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AFNI Message Board
Once I removed the -giant_move option, @SSwarper worked for this subject. I hope this helps.
by
krisknut
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AFNI Message Board
Okay, I see. Without any clustering, there is one voxel that does appear at q= .05. Thanks for the explanation.
by
krisknut
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AFNI Message Board
The output results for q-value of my 3ttest++ on resting state data with two groups (healthy volunteers vs patients), two visits combined, using resting state scans, does not match the results using the afni display.
I used this gen_group_command.py:
# Compare all 100s vs 300s, combined visits, run 2
gen_group_command.py -write_script analysis_script.tt.100s_vs_300s_AllV_R2 -command 3dttest+
by
krisknut
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AFNI Message Board
I'm having a similar problem. Any solutions found? Thanks.
by
krisknut
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AFNI Message Board
Here's the full listing for the command run:
********* Starting @SSwarper for TDT_101 Visit1 ************
******************************************
Running .cshrc
++ Starting: @SSwarper v2.2
++ Default OMP_NUM_THREADS is 12
++ Based on input, the output directory will be:
.
++ SSW Step 1
++ 3dUnifize: AFNI version=AFNI_20.1.06 (May 4 2020) [64-bit]
*+ WARNING: If you a
by
krisknut
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AFNI Message Board
While running @SSwarper, I get a Fatal Error after the following:
++ 3dAllineate: total CPU time = 2446.8 sec Elapsed = 1214.6
++ ###########################################################
++ # Please check results visually for alignment quality #
++ ###########################################################
++ # '-autoweight' is recommended when using -lpc or -lpa #
++
by
krisknut
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AFNI Message Board
Re: differences between afni_proc.py example 6 and example 11:
The help text for afni_proc.py now says Example 11 is no longer recommended for a complete analysis.
Is Example 11 still recommended for resting state or not? It's not clear what is meant by "for a complete analysis" or what is wrong with example 11.
by
krisknut
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AFNI Message Board
When I open a terminal window and type "afni", I get the following error. Note that I've put echo statements in my .bash_profile and .bashrc to verify they are being called and setting DYLD_LIBRARY_PATH correctly (I did this in response to the error, so know they are not causing the error):
Last login: Fri Feb 7 10:03:51 on ttys001
Running .bash_profile
RUNNING ~/.bashrc
--
by
krisknut
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AFNI Message Board
I'm getting a Segmentation fault: 11 when I run afni_system_check.py -check_all. Here is the output:
~: afni_system_check.py -check_all
-------------------------------- general ---------------------------------
architecture: 64bit
system: Darwin
release: 18.7.0
version: Darwin Kernel Version 18.7.0: Sat Oct 12 00:02:19 PDT 2019; root:x
by
krisknut
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AFNI Message Board
Yep, updated afni today, and @auto_tlrc is now found and working. Thanks.
by
krisknut
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AFNI Message Board
afni -ver
Precompiled binary macos_10.12_local: Aug 27 2019 (Version AFNI_19.2.20 'Claudius')
which @auto_tlrc
(returns a blank)
by
krisknut
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AFNI Message Board
I'm getting this error message when running afni_proc.py:
#Script is running (command trimmed):
3dcopy /Users/kk/abin/MNI152_T1_2009c+tlrc ./base.nii
++ 3dcopy: AFNI version=AFNI_19.2.20 (Aug 27 2019) [64-bit]
#++ Aligning /Volumes/shares/.../New_analysis/CFS_325/Visit1/CFS_325_Visit1_RS123/1/CFS_325.Visit1.1.results/awpy/base.nii data to /Volumes/shares/.../New_analysis/CFS_325/Visi
by
krisknut
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AFNI Message Board
Note that the last line of the results of 3dinfo for a resulting bad mprage file is:
Dataset created via: @auto_tlrc -base TT_N27+tlrc -input S06_MPRAGE+orig -no_ss
and the last 3 lines for a good mprage are:
Dataset created via: @auto_tlrc -base TT_N27+tlrc -input S38_MPRAGE+orig -no_ss
3drefit -view +tlrc __ats_tmp___upad40_S38_MPRAGE+orig.HEAD
3drefit -wset S38_MPRAGE+orig __ats_tmp___u
by
krisknut
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AFNI Message Board
I'm trying to run @auto_tlrc on resting state data, using
@auto_tlrc -base TT_N27+tlrc -input ${Subject}_MPRAGE+orig -no_ss -OK_maxite
I've also tried without the -OK_maxite option. Sometimes the command works and other times it fails, and I can't figure out why.
I get *** ERROR: failed (35) to open file ./__ats_tmp___upad40_S38_MPRAGE+tlrc.HEAD for attribute writing;
by
krisknut
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AFNI Message Board
I got rid of the Label and used a covariates file consisting of:
Subject Age TT
S08 30 600
etc.
and that worked with the command:
3dttest++ -setA S \
S08 S08.rest.3dTcorrMap.z+tlrc.BRIK \
etc.
-prefix Results_ -mask mask+tlrc. -covariates covariates.txt
by
krisknut
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AFNI Message Board
The covariates are of the format:
Subject Age TT Labels
S08 30 600 S08.rest.3dTcorrMap.z+tlrc.HEAD
S09...
I've also tried:
Subject Age TT Labels
S08 30 600 S08.rest.3dT
S09...
and got:
Analysis_TT_age: 3dttest++ -setA 'S??.rest.3dTcorrMap.z+tlrc.BRIK' -prefix testing -mask clip_group_brainTissueMask_tSNR10_count_no19+tlrc. -
by
krisknut
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AFNI Message Board
I see that the command is using the first 12 characters rather than the whole name, but I suspect some other problem is occurring too. I'm new to 3dtest++ and find the necessary syntax of the covariates file and the mapping between the 3dttest++ command unclear.
Here's the error message:
3dttest++ -setA 'S??.rest.3dTcorrMap.z+tlrc.BRIK' -prefix testing -mask clip_group_
by
krisknut
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AFNI Message Board
That worked! Many thanks.
I corrected it to:
./McRetroTS 46.resp 46.puls 3 43 50 0
by
krisknut
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AFNI Message Board
Without the t-shifting and detrending (using the original oba.slibase.1D instead):
file_tool -test -infile oba.slibase.1D -->
oba.slibase.1D has 0 bad characters
oba.slibase.1D file type: UNIX
1d_tool.py -show_rows_cols -infile oba.slibase.1D -->
rows = 153, cols = 1950
and when I rerun my afni_proc.py, I get a similar error with different values:
** ERROR: ricor nsliregs x nslic
by
krisknut
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AFNI Message Board
I'm getting the following error: ** ERROR: ricor nsliregs x nslices != nvec (0, 43, 13)
(0 ricor slices, 43 volume slices, 0 slice 0 labels)
when executing command:
afni_proc.py -subj_id subj046 -script proc.subj046 -scr_overwrite \
-check_setup_errors yes -check_results_dir no -blocks despike ricor \
tshift align tlrc volreg blu
by
krisknut
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AFNI Message Board