Show all posts by user
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 1 Pages: 1
Results 1 - 22 of 22
Dear Gang,
Thank you for the comments.
Now I understand whole issues that I had..
I think I confused with the beta-hat, which is the regression coefficients from each subject.
Again, I really appreciate for your consistent explanation (thank you so much).
Regards,
dawoon
by
dawoon
-
AFNI Message Board
Dear Gang,
Thank you so much for your detailed and kind answers.
However.. I still have some questions...
First, to summarize..
- Beta and t-statistics values from GLT is input for measuring MEMA, and it's output is 'a' (i.e., group effect) and their t-statistics.
From this point.. I thought using a, x, subject-specific error, sampling error, etc.,
the MEMA will be meas
by
dawoon
-
AFNI Message Board
Dear Gang,
Thank you for your comments.
I think I should write it more detail and generally.. my apologies.
Regarding your comments, I wrote the related question in green color.
Again, thank you for the kindness comments.
1. By "individual beta map" do you mean that voxel-wise statistical significance for each subject? If so, you already have that information from your individu
by
dawoon
-
AFNI Message Board
Dear Gang,
Thank you for your answer.
However, I have another several question..
- Background knowledge which I understood
From the paper, I understood that the MEMA is one of the group level inference (am I right?)..
Also the method of the MEMA is to estimate beta value with considering the subject variability.
By the estimated beta value using MEMA (beta = sum(alphai * xi) + delta; ap
by
dawoon
-
AFNI Message Board
Dear Gang,
I appreciate for your comments. I understood about the main effect but I still have a problem related to the MEMA..
I tried to find out, however I couldn't figure out which shows the MEMA beta value..
Thus, as you mentioned.. I brought the command line result.
path/test.001.3dMEMA/test.results> 3dinfo -verb ./data+tlrc.HEAD
++ 3dinfo: AFNI version=AFNI_17.0.04 (Jul 2
by
dawoon
-
AFNI Message Board
Dear expert,
Hello, I would like to ask about the estimated beta values from 3dMEMA.
I also tried to check the AFNI message board, and I could find that we can't get the residual from 3dMEMA currently.
However, I'm not sure whether that is the one, which I wanted to check.
Therefore, the questions which I want to ask are:
[1]
I read the paper related to the MEMA.
I could find
by
dawoon
-
AFNI Message Board
It was solved after removing the space and some back slash ('\')..
It seems that the space was the issue that I had.
Thank you..
Dear AFNI experts,
Hello, I'm trying to conduct 3dREMLfit using concatenated data for conducting 3dMEMA.
(Following the paper "FMRI group analysis combining effect estimates and their variances." (Chen, Gang, et al., 2012))
The conc
by
dawoon
-
AFNI Message Board
Dear AFNI experts,
I'm trying to conduct the 3dDeconvolve.
The data which I used is the concatenated pre-processed data (i.e. concatenated two runs; also I concatenated motion part too.)
The problem is, there were no issues in other subjects data, but only one subject data had an issue.
The error message was shown below.
** AFNI version = AFNI_17.0.04 Compile date = Jul 26
by
dawoon
-
AFNI Message Board
Dear AFNI expert,
I have three additional question related to the tshift, @auto_tlrc, and wm/csf regressing part.
(My apologies in advance, it could be easy/irritating questions...)
The reason is, I thought that it is okay to use, but I heard it is difficult to say correct or not to use in pre-processing from my supervisor..
Thus, may I ask you whether it is okay to use?
The code is shown
by
dawoon
-
AFNI Message Board
Dear Rick,
Thank you for the detailed comments/advices.
It really helped to understand more about the TSNR and the mask related part.
Again, thank you so much.
Regards,
DaWoon
by
dawoon
-
AFNI Message Board
Dear AFNI experts,
Hello, I'm trying to determine the pre-processing steps for my data.
However, it is still not clear for me whether I'm right or not.
Also, there are several steps that I want to ask.
The below is the questions which I want to ask.
1. I tried to conduct detrend after 'scale'.
However, when I check the 'TSNR average', the value seems t
by
dawoon
-
AFNI Message Board
Dear rick,
Thank you for the comment.
I found that "-inweight -init_xform AUTO_CENTER" options in @auto_tlrc part could help to get correct shape of the brain.
Thank you :)
Regards,
dawoon
by
dawoon
-
AFNI Message Board
Dear Gang,
Thank you for the confirmation and additional information related to the PPI analysis.
It's really helped me to understand more. Thank you :)
Regards,
DaWoon
by
dawoon
-
AFNI Message Board
Dear AFNI experts,
I have an question regarding the alignment.. (actually, I'm not fully sure that it is related to the alignment..)
Not all the subjects, but only one subject shows different brain shape after pre-processing.
(You could find the image in the attachment [(A): different one, (B) normal one].)
When I tried to check the step, it seems that it has an issue in 'align&
by
dawoon
-
AFNI Message Board
Dear AFNI experts,
I am looking for some advice regarding process the PPI analysis.
I followed the steps from ";.
However, I'm not sure that I conducted right, and there was several questions, which I didn't understand.
(Even I checked the "-help" part, and so on.)
- despike, retroicor, tshift, align, tlrc, volreg, blur, mask, detrend, scale
1. Generated a
by
dawoon
-
AFNI Message Board
Dear Rick,
Thank you so much for the comments.
It's really helped me to understand and conduct AlphaSim (-Clustsim).
Thank you again! :)
Best,
DaWoon
by
dawoon
-
AFNI Message Board
Dear AFNI experts,
I am looking for some advice regarding process the 3dClustSim (forgive me if my question is too basic..).
I tried to conduct AlphaSim, and I could find that 3dClustSim is one of the method to measure it.
However, I also found the another way to measure.
1. Input an option '-Clustsim' during conducting 3dttest++
3dttest++ -prefix prefix_name -AminusB -pair
by
dawoon
-
AFNI Message Board
Dear AFNI experts,
I am looking for some advice to extracting beta values from specific brain area.
There are two questions, one is generating a mask, and the other one is extracting the beta values
(I'm new to this part, so forgive me if my question is too basic..)
Steps which I did:
1. Extract cluster, where I am interest in, from ANOVA result:
3dclust -1noneg -1thresh 0.05 -
by
dawoon
-
AFNI Message Board
Dear Rick,
Thank you for the comment!
Even I checked the script more than three times, I didn't realize that I missed the '\' at the end of the prior line..
Thanks!
DaWoon
by
dawoon
-
AFNI Message Board
Dear Gang,
Thank you for the comments.
Actually, there are 20 subjects in my data, and I tried to conduct the 3dANOVA3.
However, I had an issue in the "-bucket", and below is the script which I used.
================================================
set dirA = /path/to/anova/data
3dANOVA3 -type 4 \
-alevels 2 \
-blevels 2 \
-clevels 20 \
-dset 1 1 1 "$dirA/stat
by
dawoon
-
AFNI Message Board
Dear AFNI experts,
I am looking for some advice to modeling the ANOVA (i.e. 3dANOVA3) in appropriate way.
(Before starting.. I'm just a beginner in AFNI.. so there could be many mistakes, issues, etc. on understanding of the function..)
In short, there are three factors in my data: factor1 - types (E, S) / factor2 - conditions (A, S) / factor3 - subjects (total 5; s01 ~ 05)
-----------
by
dawoon
-
AFNI Message Board