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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, I am to use motion regressors on a run by run basis in 3dDeconvovle. With -local_times I can have each of 6 runs read as starting from each line, but when I do the same for movement regressors like the following:
-stim_file 9 movement_regressor1.txt -stim_base 9 -stim_label 9 mmx
I get the error:
WARNING: 1D file movement_regressor1.txt has 6 rows and 556 columns: ignoring late
by
3dFoodie
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AFNI Message Board
Hi,
I want to run glts with 3dDeconvolve on subjects that have variable amounts of useable data, including subjects who have no data for some conditions. In the example below, for example, if a subject has no data for CalmGo how would that affect the glts that include that regressor as specified below? Would a 0 be included for each GLT, or would they be ignored and the other GLTs reweighted
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3dFoodie
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AFNI Message Board
OK thanks, do these seem like reasonable parameters (in bold)?
3dFWHMx -ACF -input SC01907_EGNG_SIEMENS_s1_EmoXResp_ErrXResp_SPMG3_errts_bucket+tlrc++ start FWHM calculations
+ FWHM done (0.00 CPU s thus far)
++ start ACF calculations out to radius = 18.95 mm
-mask ~/Masks/ + ACF done (0.00 CPU s thus far)
# old-style FWHM parameters
6.28651 6.47933 6.19718 6.31992
# ACF model
by
3dFoodie
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AFNI Message Board
Thanks, but I am having confusing results with this. When I run 3dFWHMx on my errts file
3dFWHMx -input SC01313_EGNG_SIEMENS_s1_Emo_RespXErr_SPMG3_errts_bucket+tlrc -ACF
# ACF model parameters for a*exp(-r*r/(2*b*b))+(1-a)*exp(-r/c) plus effective FWHM
0.961511 3.20408 7.81402 7.72251
Other errts files from this data set give similar results. Then from 3dClustSim I get:
3dClustS
by
3dFoodie
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AFNI Message Board
Hi, what is currently the recommended way of using 3dClustSim for cluster thresholding? Is there an example I could refer to?
Thank you
by
3dFoodie
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AFNI Message Board
Hello, I am wondering when a GLT contrast is run in 3dDeconvolve such as:
-gltsym 'SYM: +1*CalmGo[1] +1*FearGo[1] +1*HappyGo[1] -1*CalmNoGo[1] -1*FearNoGo[1] -1*HappyNoGo[1]' -glt_label 11 Go-Nogo \
where each of these specified are stim_labels run with function SPMG3, is the variance around each of the lower level betas taken into account for estimating the beta and variance of t
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3dFoodie
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AFNI Message Board
Maybe I can explain the analysis that I am hoping to do based on behavioral results for better clarification on how to model the imaging data with 3dMEMA or another program if necessary (I have used 3dMVM and 3dLME but would rather use 3dMEMA if possible).
I have two groups of subjects (BN and HC). They differ behaviorally on the task with respect to age (so I am looking for an interaction) an
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3dFoodie
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AFNI Message Board
The groups do not contain the same number of subjects. Should I still use -1 and 1 or should the average = 0? Does that mean subjects in the smaller group will end up weighted more (i.e. 1.1 vs -0.9)?
If I try to compare the groups as different sets, 3dMEMA fails, and I get this error:
Error in process.MEMA.opts(lop, verb = lop$verb) : bad length for subjLab
Also, I am interested in the
by
3dFoodie
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AFNI Message Board
Hello, I am trying to run the 3dMEMA code below. When I try to use the mask listed I get the following error:
Error in if (is.na(size)) { : argument is of length zero
Calls: process.MEMA.opts -> read.AFNI
In addition: Warning messages:
1: In readLines(conhead) : line 1 appears to contain an embedded nul
2: In readLines(conhead) : line 194 appears to contain an embedded nul
3: In readLi
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3dFoodie
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AFNI Message Board
Hi, I want to run 3dMEMA on a subject sample that includes subjets belonging to two groups, but rather than comparing groups I want to control for group. Is it possible to include a categorical covariate? Or Could I just dummy code 1 and 2 (or 0 and 1) for group membership and not center?
Thank you
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3dFoodie
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AFNI Message Board
Yes, I believe the effects may be different between runs, and I would also like to include subjects with only partially usable data. On the one hand I could see including more subjects and anlyzing data separately being an advantage in estimating variance, but on the other hand including subjects who do not have full data sets or only have the minimum number of correct trials to analyze may resul
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3dFoodie
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AFNI Message Board
Hi, I am trying to decide how to break down data for analysis for a tfMRI task with 6 runs, and I was wondering if it would be preferred to analyze each run separately and put them into a group level analysis, or if it is better to analyze all runs for each subject all together. The advantage of the former method would be better separation of trial conditions, but the disadvantage is each run wil
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3dFoodie
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AFNI Message Board
Can you please comment on how to make the decision of 1- vs 2-sided thresholding for F maps or for general linear tests that do not have a directionality or "sidedness"? for example if I have a F-stat map for age and also a general linear test for age (i.e. -gltCode 1 'Age : ') then what would be the recommended thresholding to use? Also I'm confused why the number of adj
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3dFoodie
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AFNI Message Board
Can you please comment on how to make the decision of 1- vs 2-sided thresholding for F maps or for general linear tests that do not have a directionality or "sidedness"? for example if I have a F-stat map for age and also a general linear test for age (i.e. -gltCode 1 'Age : ') then what would be the recommended thresholding to use? Also I'm confused why the number of adj
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3dFoodie
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AFNI Message Board
Great.
Sorry I thought it was attached, but I guess txt files don't attach here. I've pasted the beginning and end without all the calculations output below. If you'd like to see everything please let me know and I will send.
So any idea what those warnings are? OK to ignore?
Thanks a lot
Running GLM
*+ WARNING: '-stim_times 2' didn't read any good times f
by
3dFoodie
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AFNI Message Board
Hi, is it possible to have a bsVar and a wsVar in MVM without the interaction between them? As in bsVar+wsVar rather than bsVar*wsVar?
Thanks,
Michael
by
3dFoodie
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AFNI Message Board
Thanks, here is the output of the command:
BN100_CalmGo.1D has 0 bad characters
BN100_CalmGo.1D file type: UNIX
BN100_CalmNoGo.1D has 0 bad characters
BN100_CalmNoGo.1D file type: UNIX
BN100_Errors.1D has 0 bad characters
BN100_Errors.1D file type: UNIX
BN100_FearGo.1D has 0 bad characters
BN100_FearGo.1D file type: UNIX
BN100_FearNoGo.1D has 0 bad characters
BN100_FearNoGo.1D
by
3dFoodie
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AFNI Message Board
Hi, I'm getting the following warnings when I run 3dDeconvolve:
*+ WARNING: '-stim_times 2' didn't read any good times from file 'BN100_HappyGo.1D'
*+ WARNING: '-stim_times 3' didn't read any good times from file 'BN100_FearGo.1D'
*+ WARNING: '-stim_times 4' didn't read any good times from file 'BN100_CalmNoGo.1D'
by
3dFoodie
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AFNI Message Board
Hi,
I'm trying to extract an ROI from a mask that contains several distinct ROIs. I understand that I can select it in some programs with the -mrange option or that programs like 3dROIStats will give values for each ROI, but it would be easier for me to create separate files for each ROI. Is there a simple way to do this?
Thanks a lot,
Michael
by
3dFoodie
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AFNI Message Board
Hi, I'm running GLMs for a higher level analysis and I compared using GAM to the amplitude sub-brik of SPMG3. The results are somewhat different. I'm wondering if there are any strong opinions about what is optimal to use if my main interest is detecting strength of activation. I haven't found much debate on this, so I cannot see what to base a decision on.
Thank you
by
3dFoodie
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AFNI Message Board
Basically, I am confused how I got an interaction effect for Age * Emotion using 3dMVM but cannot find that effect on any post-hoc tests I've done. In 3dMVM I used the option -wsE2 because Emotion has 3 levels, although now I am seeing that in the 3dMVM help page there is conflicting information on this option. In one place it says:
"This option only makes sense if a within-subject f
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3dFoodie
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AFNI Message Board
OK thank you. I thought maybe these tests were comparing the effects of emotion at mean centered age, but you are saying these compare the slopes of age between emotions?
Thanks,
Michael
by
3dFoodie
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AFNI Message Board
Sorry, I mean age as a quantitative variable. Really this question is about quantitative variables in general. If this were in R, I would would look for the interaction effects Age : Emotion using lmer so see how a unit increase in age predicts the DV on an emotional face relative to a baseline face.
In afni I know how to find an interaction of emotional face type by age as a quantitative vari
by
3dFoodie
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AFNI Message Board
Hi, I'm wondering how to code general linear trends within 3dMVM (or another program if there's a better one) as a function of a quantitative variable. For example if people are looking at afraid and calm faces across a developmental population, and I want to see if the difference in activation between afraid and calm faces changes as a function of age, how would I code that? My underst
by
3dFoodie
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AFNI Message Board
Hi,
I'm running 3dDeconvolve on subjects based on correct responses in a task, meaning that subjects have different numbers of events being considered in the estimation of their beta weights for each condition. When I bring the output of these GLMs to higher level modeling like 3dMVM or 3dLME, will the variance or uncertainty of these parameter estimates be taken into account or are all p
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3dFoodie
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AFNI Message Board
Thank you for the response. When I change it to either of those I get the same error. In addition, I tried running it with 3dMVM. and still got the error below. Any suggestions would be appreciated. Thanks.
Error in if (len%%wd != 0) errex.AFNI(paste("The content under -dataTable is not rectangular !", :
argument is of length zero
Calls: process.MVM.opts
Execution halted
The
by
3dFoodie
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AFNI Message Board
Hi, I am trying to run a 3dLME, and am getting there error:
Error in if (len%%wd != 0) errex.AFNI(paste("The content under -dataTable is not rectangular !", :
argument is of length zero
Calls: process.LME.opts
Execution halted
I posted my command and dataTable below. I cannot find any problem with it. Any suggestion how to fix this please?
Thanks!
3dLME -prefix C
by
3dFoodie
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AFNI Message Board
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