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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
Results 1 - 30 of 33
Does anyone know an easy way to set all non-zero values to "1" or any other user specified value in mask dataset? I have searched and tried many different things but still have not been successful.
by
adjacobson1
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AFNI Message Board
Unfortunately, I am still getting the same error:
Have lop$centerType 1
Have lop$centerVal 28 for bmi
Warning message:
In cbind(lop$xMat, lop$covData) :
number of rows of result is not a multiple of vector length (arg 1)
Warning in DOF.check.MEMA(lop) : Too few subjects for options selected.
Error:
Execution halted
by
adjacobson1
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AFNI Message Board
Precompiled binary macosx_10.6_Intel_64: Nov 19 2014 (Version AFNI_2011_12_21_1014)
I am updating now.
by
adjacobson1
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AFNI Message Board
Hello. I am having an issue with 3dMEMA with a covariate that I have been unable to solve. Can anyone see what I am doing wrong? The message is:
Have lop$centerType 1
Have lop$centerVal 28 for bmi
Warning message:
In cbind(lop$xMat, lop$covData) :
number of rows of result is not a multiple of vector length (arg 1)
Warning in DOF.check.MEMA(lop) : Too few subjects for options selected.
by
adjacobson1
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AFNI Message Board
This is what came back when I entered the following command: 3dinfo -space TT_N27 my_file+tlrc
NO-DSET
ORIG
I used 3drefit and it solved the problem. Thank you so much! You saved me a lot of hassle!
by
adjacobson1
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AFNI Message Board
Hello:
I recently used 3dMEMA to analyze a dataset and I am unable to use the whereami program to obtain a list of the regions in each significant cluster after applying a threshold. Is this a known issue? Am I missing something? I have always been able to use whereami after analyzing with 3dttest++ and I really like this feature. Any help would be greatly appreciated. Thanks!
by
adjacobson1
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AFNI Message Board
Hello:
I ran 3dttest++ on a group of subjects and added BMI as a covariate. I am viewing the effect of BMI in the GUI and I have set a threshold, etc… After "clusterize" I am given many significant clusters…. but the clusters do not represent "activation", correct? They represent brain regions that are influenced by the covariate (BMI)?
The "max intensity" of
by
adjacobson1
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AFNI Message Board
Right now it is pilot data and we only have one subject. Is it possible to determine significance with a single subject with any certainty?
by
adjacobson1
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AFNI Message Board
Thank you Gang and Rick! This has been very helpful information in my quest to learn this analysis.
I do have another question:
I have many regions that are correlated at r = .4 ish… How do I determine the significance (p value) for the correlation values? I cannot think of an easy way to determine this value.
by
adjacobson1
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AFNI Message Board
Thank you Gang and Rick! This has been very helpful information in my quest to learn this analysis.
I do have another question:
I have many regions that are correlated at r = .4 ish… How do I determine the significance (p value) for the correlation values? I cannot think of an easy way to determine this value.
by
adjacobson1
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AFNI Message Board
Thanks!
I am looking at the data and I am interested to find that the correlation between the seed region and the seed region (when the seed region was also included in the ROI mask) is 0. I would have expected it to be 1. Does it make sense for it to be zero?
by
adjacobson1
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AFNI Message Board
Thanks so much for the info!
I have another question:
The end result that I am getting is a correlation coefficient for each of the regions that I selected. This is what I was hoping for. In my understanding, the correlation is referring to the relationship between my seed region and the selected region. Is there an easy way to also examine the relationships between the regions that are co
by
adjacobson1
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AFNI Message Board
I went through all of the steps to run context dependent correlation analysis on one subject. I realize that a group analysis would be preferable but I am looking at pilot data with one subject to get an idea of how this analysis works. Everything appears to have run correctly. I created a dataset that contains all of the correlations between the seed region (Left Insula) and the rest of the epi
by
adjacobson1
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AFNI Message Board
Thanks so much! This is very helpful! Our ISI is 10 seconds and we use BLOCK(8,1) currently. We tried the TENT function but we decided that our ISI was not long enough. Do you agree?
by
adjacobson1
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AFNI Message Board
I am having a difficult time figuring out how I can extract the peak amplitude of the IRF in a specific region, for each time the stimulus was presented (separately). I can get the peak amplitude of the average of all of the stimulus presentations but I would like to get the peak amplitude each time the stimulus is presented. Does anyone know how I can do this?
by
adjacobson1
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AFNI Message Board
Correction:
The problem is occurring in 3dmaskave:
3dmaskave -mask ROI_L_INSULA_SEED_3mm_0.2+tlrc pleas_1_${STATE}_scaled+tlrc > ${ID}_${STATE}_R1_L_INSULA_SEED.1D
by
adjacobson1
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AFNI Message Board
Hello:
I am using 3dDetrend in my PPI analysis and I am running into an issue with the 1D files that it creates. here is the command I am using:
3dDetrend -polort 1 -prefix ${ID}_${STATE}_R1_L_INSULA_SEED_R ${ID}_${STATE}_R1_L_INSULA_SEED.1D\'
What I want is the values in the time series after removing the trend but what it gives me is the values along with the number o
by
adjacobson1
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AFNI Message Board
Thanks for your help!
I have the 3dDeconvolve running smoothly now. When viewing the data in the AFNI GUI i am a little confused. I think that I am supposed to me looking at the activation map from the interaction regressor. Is that correct? From what I have read, that is the variable of interest. But when I am viewing the data I am not sure what to set as the OLay and Thr in the drop down me
by
adjacobson1
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AFNI Message Board
I used the -v option and it seems to have done the trick. Does that seem like a good way to do it?
by
adjacobson1
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AFNI Message Board
Thanks Rick! I am having trouble with "cat" as I have never used it. This is my command so far:
cat LG_h_R1_L_Scaled_INSULA_SEED_SUC_Inter_ts.1D LG_h_R2_L_Scaled_INSULA_SEED_SUC_Inter_ts.1D > LG_h_2Runs_L_Scaled_INSULA_SEED_SUC_Inter_ts_cat.1D
What I am hoping for is a .1D file with one column of data that is in this form:
Run1
Run1
Run1
Run1
Run 2
Run 2
Run 2
Run 2
by
adjacobson1
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AFNI Message Board
Thanks! I realized yesterday that my concatenated runs were in two columns. Maybe cat will solve that. Should I also change the -dt 2 to -dt (total TR's in the run)?
waver -dt 2 -GAM -inline 1@1 > GammaHR.1D
by
adjacobson1
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AFNI Message Board
I am trying to learn the process of Context-Dependent Correlation Analysis in order to investigate functional connectivity. For this example I am using the L INSULA as the seed region in one subject (LR). I have been following the steps outlined by Gang (which have been sooo helpful) but I am running against a few issues that I do not know how to solve. Any help would be greatly appreciated.
by
adjacobson1
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AFNI Message Board
I am noticing that many of my subjects have motion artifact that is strongly affecting my data. Motion correction using 3dregistration has been done in the preprocessing, and censor tr has been used to eliminate tr's with motion greater than 2 mm, but my problem persists. I am ending up with negative (blue) horizontal slices that are very clearly related to motion. I am thinking of reducing
by
adjacobson1
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AFNI Message Board
In the current study in my lab, we are having a difficult time obtaining significant results from a group analysis of older adults. We have examined the data in multiple ways and have come to the conclusion that there is definitely per-subject activation but when the subjects are grouped, the variability in the data results in zero significant clusters. I understand that in order to find signific
by
adjacobson1
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AFNI Message Board
After some deeper digging I realized that the original processing protocol was written so that the stimulus time started 2 seconds late in the stim_timing file. This was how the 2 seconds during swallowing was eliminated. With the stimulus timing file beginning 2 seconds later than the actual stimulus onset, setting a block of 8 for a 10 second block makes more sense. Still I wonder, is this an O
by
adjacobson1
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AFNI Message Board
Thanks so much for the response! have been away from the office and just had time to read it. I will be examining the data that you suggested.
I thought of another potential issue with our data:
Here is our generic 3dDeconvolve:
3dDeconvolve -input SUBID_pleas_h_2runs+tlrc \
-concat '1D: 0 360' \
-mask pleas_h_full_mask+tlrc \
-censor /volumes/ARIANA_HD/Users/cmurphy/Deskto
by
adjacobson1
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AFNI Message Board
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