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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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Thanks Gang, I must have been looking at the wrong section where it explains each basis function.
Regarding the duration, 3dDeconvolve help shows you can add the stimulus duration to the modeling for SPMG. For example, if you have a 6-second stimulus, you could enter SPMG(6). I was wondering if the output has the duration modeled separately, but after looking at it, I see it doesn't.
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Danny
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AFNI Message Board
SPMG3 - 7 years ago
Hey AFNI experts,
I had a basic question regarding the SPMG3 option for 3dDeconvolve. I was wondering what the interpretation is for each of the 3 parameters (and their respective output sub-briks). I noticed in the 3dDeconvolve help, that SPMG2 is the gamma variate with the temporal derivative and the dispersion derivative. I don't see it documented in the help what the added parameter f
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Danny
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AFNI Message Board
Hi AFNI Experts,
I am planning on running AFNI_proc.py, and was wondering if the 3dFWHMx/3dClustSim "-acf "(or -ACF) option is automatically applied, or if it needs to be specified? I couldn't find the -acf option when I searched the help page for AFNI_proc.py.
If it needs to be specified, would it be after a command like this: "-regress_blur_errts -acf" ?
Thank
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Danny
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AFNI Message Board
Thanks Colm and Gang!
The 3dDetrend -polort 0 command seems the easiest to use and script. I didn't realize this command would demean without removing the other trends in the data.
Thanks!
-Danny
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Danny
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AFNI Message Board
Hi AFNI Experts,
I was wondering what the best command would be to use for demeaning a beta-series bucket file (i.e., each sub-brik corresponds to an individual trial coefficient) that I converted into a "3d+time-like" file?
I know "1d_tool.py -demean" can be used on .1D files, but I am having a hard time finding the command for 3d+time files...
Thanks,
Danny
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Danny
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AFNI Message Board
I should demean before I extract my betas from a seed region? Should I use something like 3dSetupGroupInCorr to do something like this? Or is there a better tool to demean my beta_bucket.nii file?
I was originally using 1d_tool.py on the extracted betas from my seed.1D file to do this.
Thanks,
Danny
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Danny
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AFNI Message Board
I will try the 3dTcorr1D and see how it goes.
Would I demean the Seed file, the beta 3d+time file, or both?
Thanks!
-Danny
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Danny
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AFNI Message Board
I will remove the additional polort. Would adding in the additional polort lead to any of the odd patterns I am finding?
You recommend using 3dTcorr1D instead of 3dfim+?
So something like:
3dTcorr1D -pearson ConditionA_Betas.nii Seed_betas.1D -prefix ConditionA_BetaSeries_CorrelationMap.nii
Thanks for all your advice and help!
-Danny
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Danny
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AFNI Message Board
Basically, I am doing the following steps in separate scripts to conduct a beta-series context dependent correlation analysis:
1) 3dDecon with IM option to get individual regressors for each condition
2) Extract betas from conditions of interest to create a beta file using 3dbucket
-This creates a separate file for betas of interest for each trial (e.g., ConditionA_betas.nii)
3) E
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Danny
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AFNI Message Board
Thanks Rick!
Would using 3dfim+ still give me the information I need? Basically, I need to correlate my beta-series 3d+time data sets with a beta-series seed region (e.g., Seed_betas.1D). The problem is that I am restricting it to correct trials only, so the number of betas per subject will differ. Would 3dDeconvolve still handle the different number of "time-points" in the beta-seri
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Danny
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AFNI Message Board
Hello AFNI Experts,
I am in the process of running a beta-series analysis to see how a seed region correlates with activity across the brain on a trial-by-trial basis. I used 3dfim+ to create the correlation map. I am wondering whether the ideal file needs to be in a column or row format?
thanks,
Danny
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Danny
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AFNI Message Board
Thanks Gang, I will use 3dbucket.
A follow up question, I didn't notice an explanation on your gPPI page regarding why you need to run the steps within each run. I am wondering what the overall benefit is of doing this within-run? Are there any references you can point me to on this?
The reason why I ask is because I was planning on completing the beta-series analysis in the same manne
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Danny
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AFNI Message Board
Hi AFNI Experts,
I am planning on running a beta-series analysis. It was suggested to me that I should run this analysis within-runs, sort of like the steps for gPPI. My question is, when should I concatenate the beta-series files into a single file for the correlation (connectivity) analysis? I was orginally going to concatenate the runs after making it a 3d+time dataset (using 3drefit) and b
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Danny
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AFNI Message Board
Hi AFNI Experts,
I recently ran a gPPI analysis. I am now wanting to extract the betas (or z-scores) into a text file, so that I can correlate the gPPI index at a target region with offline self-reported measures of anxiety. I believe that 3dttest++ does something similar if I use a covariate file with the anxiety measures.
But I want to instead extract the values into a text file and crea
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Danny
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AFNI Message Board
Thanks Gang!
I wanted to make sure I am on the correct path with the gPPI!
Thanks,
Danny
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Danny
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AFNI Message Board
Hi AFNI Experts,
I have a question about the generalized approach to the context-dependent correlation analysis (aka PPI). I noticed on Gang’s page, it says that steps 1 & 3 are identical to the standard PPI, but then says “follow steps 2, 4, and 5 except that at step 4 there are no more -1s.” Looking at step 4, it says “if you only consider one condition A, code the condition with 1’s and
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Danny
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AFNI Message Board
Hi Gang,
Thanks for the response. I have a follow-up question.
For running 3dttest++ on this, I am guessing I would run it with 1 set, and compare the beta-coefficients against zero?
Thanks,
Danny
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Danny
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AFNI Message Board
Hello AFNI Experts,
I recently completed a PPI analysis using Gang's set of instructions. I have a question about the output files and which sub-bucket to use in subsequent analyses at the group level. I should note that my study is within-subjects, so I am not planning on comparing two-groups. However, I do want to get a "group" average to see which brain regions correlate with
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Danny
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AFNI Message Board
Okay, it averages the signal within the clusters I specifiy from the input mask.
So, if I have 3 voxels in cluster 2 and 7 voxels in cluster 3, then when I use the '-mrange 2 3' option, it will average the signal from the 10 voxels that that are specified in '-mrange 2 3'?
Thanks,
Danny
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Danny
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AFNI Message Board
Thank you both for the helpful tips.
For running 3dmaskave with the -mrange option or the multiple selector option (i.e., '<2..3.'), does it average the clusters that are selected?
Danny
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Danny
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AFNI Message Board
Hello AFNI Experts,
I am wondering if there is a simple command to change the cluster number within a mask without having to go back and redraw or relabel the cluster number?
I created an FFA mask where I have the left and right FFAs with different cluster numbers (i.e., 2 & 3). Now I want to run analyses using them as a single bilateral cluster (i.e., 2&3 combined). Is there a way
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Danny
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AFNI Message Board
Hi Rick,
Yeah, seems odd. I have been using the mid-June 2014 binaries.
In my script where I am doing all of the pre-processing for the PPI, I added in a 2 second sleep command in between the 4 separate 1dcat commands (1 for each of the 4 runs) with the -stack option. For some reason, now it is working fine. Not sure why that would alter how the stack option works...But it seems to work, s
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Danny
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AFNI Message Board
It is not creating a single column, but creating 4 different (i.e., different values) columns with 239 time points. I checked several subjects. Not sure why it is not concatenating...
Oddly, when I run the command at the terminal window, it creates a 1 column .1D file. However, when ran in a script I created with the identical command, it did not work...
-Danny
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Danny
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AFNI Message Board
Hi Rick and Gang,
Yes there are 4 runs. I concatenated them at the end of doing all the individual runs using:
1dcat -stack option where I include each run in the command.
Danny
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Danny
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AFNI Message Board
Hi Gang,
I mispoke in my previous post. I am using them as a regressor in 3dDeconvolve:
-stim_file 21 ${subfolder/Seeds/${subject}.Seed_run_all.1D -stim_label 21 Seed_ts \
-stim_file 22 ${subfolder}/Seeds/${subject}_Interaction_term_run_all.1D -stim_label 22 Interaction_term
But I still enounter this error:
"WARNING: 1D file ${subfolder}/Seeds/sub230.Seed_run_all.1D has 239 ro
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Danny
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AFNI Message Board
Hello AFNI Experts,
I recently encountered a warning when running 3dDeconvolve for a PPI analysis. Specifically, the warning occurs when reading in the timing file for the seed and interaction regressor. There error is as follows:
"WARNING: 1D file ${subfolder}/Seeds/sub230.Seed_run_all.1D has 239 rows and 4 columns: ignoring later columns"
Does this indicate that it is omitting
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Danny
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AFNI Message Board
Hi Rick,
I did get the "if: Badly formed number" error fixed. Sorry about not mentioning that in my previous post. The error was caused by the way I changed the variable name in that command. I changed it back to how it is labeled in AFNI_proc.py. The script is now functional. I just omitted some steps that our lab didn't need (GCOR, individual level ClustSim). We plan to re-ru
by
Danny
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AFNI Message Board
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Pages: 123