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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
Page 1 of 2
Pages: 12
Results 1 - 30 of 38
Hi Rick,
1. Can you run FreeSurfer programs successfully?
Yes, FreeSurfer program runs without any issue.
2. Does "3dAllineate -help" work?
Do you mean running 3dAllineate -help on the terminal? If so, yes it works.
3. Is it suma that is failing exactly like in your initial post?
Please repost the command and output, juuuuust to be sure.
#!/bin/csh
setenv FREESURFER
by
Junyeon
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AFNI Message Board
Hi pt,
Thank you so much for the response! Unfortunately, it still has the same error even after update. Could you please let me know if there is another issue here? Below is the result of afni_system_check.py -check_all.
-------------------------------- general ---------------------------------
architecture: 64bit
system: Darwin
release: 16.7.0
by
Junyeon
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AFNI Message Board
Hi pt,
Below is the result.
-------------------------------- general ---------------------------------
architecture: 64bit
system: Darwin
release: 16.7.0
version: Darwin Kernel Version 16.7.0: Wed Feb 27 00:29:57 PST 2019; root:xnu-3789.73.43~1/RELEASE_X86_64
distribution: 10.12.6 x86_64
number of CPUs: 12
apparent logi
by
Junyeon
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AFNI Message Board
Dear AFNI experts,
I had the following error during SUMA.
Abort
dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address
Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib
Expected in: /usr/lib/libSystem.B.dylib
dyld: Symbol not found: ___emutls_get_address
Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib
by
Junyeon
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AFNI Message Board
Hi Rick,
Sorry for the belated update. My coworker suggested trying alignment of anatomical and epi images and rerun the proc py which worked. Thank you so much for your help.
Jun
by
Junyeon
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AFNI Message Board
Hi Rick,
Yes, I figured out that I had all stimuli (I,F,C) in the previous script.
-- At sub-brick #1 'C#0_Coef' datum type is float: -24.2262 to 39.3309
-- At sub-brick #4 'F#0_Coef' datum type is float: -31.3828 to 31.9878
-- At sub-brick #7 'I#0_Coef' datum type is float: -34.3002 to 53.807
-- At sub-brick #10 'I_vs_C_G
by
Junyeon
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AFNI Message Board
Hi Rick,
Thanks for the so much for the response.
Here is the result of Stimulus I vs Stimulus F 3dinfo -verb stats.subject1.Condition1+tlrc | grep Coef.
-- At sub-brick #1 'I#0_Coef' datum type is float: -2.92984 to 2.53249
-- At sub-brick #4 'F#0_Coef' datum type is float: -2.53124 to 3.31587
-- At sub-brick #7 'I_vs_F_GLT#0_Coef'
by
Junyeon
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AFNI Message Board
Hi pt,
I really appreciate your help. The below is what I got for the command you suggested for Stim I vs Stim F
hlhp-105:Proc_results_con-fix titus$ 3dinfo -nv stats.subject1.Condition1+tlrc.
10
hlhp-105:Proc_results_con-fix titus$ 3dinfo -nvi stats.subject1.Condition1+tlrc.
9
The below is what I got from Stim I vs Stim C
hlhp-105:Proc_results_con-fix titus$ 3dinfo -nv stats.subj
by
Junyeon
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AFNI Message Board
AFNI experts,
I am running proc py for functional data using stimulus files. In this dataset, there are two conditions (Condition A and Condition B), and three stimulus files (Stim I, Stim C, and Stim F). Firstly, I have compared Stim I and Stim C and the part of the proc py script was like below.
-regress_stim_labels I C \
-regress_basis 'BLOCK(1,1)' \
-regress_censor_motion
by
Junyeon
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AFNI Message Board
Daniel,
Thanks again for your help. The command line worked well. Is it converted into AFNI's MNI space? Screenshots of the overlay on MNI_152 are attached.
Thank you,
Jun
by
Junyeon
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AFNI Message Board
Daniel,
Thanks again for your help. I am sorry that @Shift_Volume is a little bit confusing to me.
First, dset should be the Nucleus Basalis mask from the SPM anatomy toolbox? I tried it the below command line but keeps showing error.
titus% @Shift_Volume -MNI_Anat_to_MNI -dset Bforebrain_4.nii -prefix MBN_mask
opref MBN_mask
++ 3dcopy: AFNI version=AFNI_18.2.15 (Aug 28 2018) [64-bit]
by
Junyeon
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AFNI Message Board
Hi Daniel,
Thank you so much for the response. I just have downloaded SPM's anatomical toolbox and tried to overlay Nucleus Basalis on MNI152 (attached files). I am not sure if this represents the accurate location of Nucleus Basalis as SPM uses different MNI template?
I read this paper (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2577158/) examining probabilistic maps of the basal fo
by
Junyeon
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AFNI Message Board
Dear AFNI experts,
I am interested in analyzing nucleus basalis of meynert, but could not find any previous paper using AFNI to analyze it. Is there any way to analyze nucleus basalis of meynert using AFNI?
Thank you,
by
Junyeon
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AFNI Message Board
Hi Gang,
Thanks so much. It works. I got following sub-bricks as the output.
#1 Training
#2 Condition
#3 Training:Condition
#4 A-B
#5 A-B t
As it is my first time to use this, I am a little bit confused to interpret the results. Is 'A-B t' the result of the difference (t-test) between Condition A*Training and Condition B*Training?
Also, there was significantly greater ac
by
Junyeon
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AFNI Message Board
Thanks Gang. What I would like to look at is the interactive effects of Condition and Training year. Am I on the right track to examine this?
by
Junyeon
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AFNI Message Board
Hi Gang,
Thanks for the help again.
3dMVM -prefix Regression \
-qVars 'Training' \
-bsVars 'Training' \
-wsVars 'Condition' \
-num_glt 1 \
-gltLabel 1 'CondtionA-ConditionB' -gltCode 1 'TST : 1*A Training : 1*A -1*B' \
-mask mask_group+tlrc \
-dataTable \
Subj Training Condition InputFile \
s1 8 A 'stats.s1.A+tlrc.BRIK
by
Junyeon
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AFNI Message Board
Hi Gang,
Thank you so much for your advice. It really helps. I have one more question to ask.
I have treated training year as a between-subject variable at first and found that the script did not run. After reading afni's 3dMVM instruction, it seems that between-subject variables are for categorical variables such as sex, genotype or group. So I have added training year as a quantitative
by
Junyeon
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AFNI Message Board
My apologies as I confused you. This study has a within-subject design where participants performed two conditions on different days. So there is no difference in covariates between conditions as those are the same for both conditions.
by
Junyeon
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AFNI Message Board
Hi Gang,
Thanks for the response. The standard deviation of training year is 11. Other variables we are also interested have SD of 23 and 70. Does this variability matter in the analysis?
Best,
Jun
by
Junyeon
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AFNI Message Board
AFNI experts,
I am currently analyzing a data where participants underwent a memory task after two conditions (condition A and B). I already have analyzed the data using 3dttest+ by comparing the difference between the two conditions. I also would like to include a covariate (year of training) to the analysis. What I can think of is to extract the activation intensities using 3dmaskave and ana
by
Junyeon
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AFNI Message Board
AFNI experts,
I am analyzing resting state data using afni proc py example 11 and am currently working on getting clustsim results for statistical analysis. I have two questions.
1) Which mask should be used for 3dClustSim result?
2) What is the difference between -fwhm and -acf?
Thank you in advance for your help,
JW
by
Junyeon
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AFNI Message Board
AFNI experts,
I am analyzing resting state data using afni proc py example 11 and am currently working on getting clustsim results for statistical analysis. I have two questions.
1) Which mask should be used for 3dClustSim result?
2) What is the difference between -fwhm and -acf?
Thank you in advance for your help,
JW
by
Junyeon
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AFNI Message Board
I see. So would you recommend me to use Example 11 (which is using Freesurfer segmentation)?
Thanks,
Jun
by
Junyeon
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AFNI Message Board
Hi Gang,
Thanks again for your help. I have used proc.py 11 for this analysis which is the most modern method. Could you please let me know why would you recommend me 9, 9b, or 10?
Thanks,
Jun
by
Junyeon
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AFNI Message Board
Hi Gang,
Thank you so much for your help. Can I have a couple of more questions?
1) Could you let me know why would you recommend 3dMVM instead of 3dLME?
2) I am wondering how to get cluester threshold for 3dMVM results. Would it be same as 3dLME?
3) Could you let me know if the steps before 3dMVM look fine?
Thank you,
Jun
by
Junyeon
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AFNI Message Board
AFNI experts,
I am analyzing resting state analysis using the seed-based method. I am interested in looking at executive function network using seed as inferior frontal gyrus. I was able to do everything correctly until proc py using poc py explanation of AFNI. However, I am not sure if the rest of the steps have been done correctly. Could you please check the below scripts and let me know if
by
Junyeon
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AFNI Message Board
Dear AFNI experts,
I am interested in analyzing cerebellum connectivity and found this parcellation in Freesurfer (http://www.freesurfer.net/fswiki/CerebellumParcellation_Buckner2011). Would it be possible to use this parcellation in AFNI resting state analysis?
Thank you,
Jun
by
Junyeon
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AFNI Message Board
Hi AFNI experts,
I am planning to attend AFNI Bootcamp this week and got an email saying have at least + 15 GB free for a laptop. Just found that my C drive has less than 15GB but has more than enough space in E drive. Would that be okay to have space in E not C drive?
Thanks,
Jun
by
Junyeon
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AFNI Message Board
Thanks again for the response. The output looks like the below.
JunyeonWon:~> echo "export DISPLAY=:0.0" >> ~/.bashrc
JunyeonWon:~> echo "setenv DISPLAY :0.0" >> ~/.cshrc
JunyeonWon:~> source ~/.cshrc
JunyeonWon:~> echo $DISPLAY
:0.0
After trying this I opened AFNI, it works. Thank you so much!
Best,
Jun
by
Junyeon
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AFNI Message Board
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Pages: 12