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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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Dear Afni experts,
I have a design consisting of responses to stimuli. I have reaction times available for each response. I wanted to use a variable epoch design with a single regressor for responses consisting of variable length blocks: 'BLOCK(RT)', where RT = is reaction time at each response.
As it is, 3dDeconvolve admits providing stimulus files of responses at, say, four time
by
cmehta
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AFNI Message Board
As a follow-up question, I am running a Mixed Effects model for testing moderating effect of a risk factor X on differences in activations across three conditions of increasing difficulty, that is,
> Y(i,t) ~ t + X + t:X + (1 + t | subject)
where Y(i,t) is estimated beta at a given voxel from subject-level processing for subject i in condition at levels t=0,1,2 of difficulty. The random
by
cmehta
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AFNI Message Board
Hi AFNI Experts,
I have processed resting state scans using afni (standard pipeline with bandpass filtering) for a group. I was examining the ss_review outputs and noticed a significant positive relationship between GCOR (average pairwise correlation in errts) and average motion. In my sample, gcor and average motion (after censoring) had 0.4 correlation.
In group analysis, would the inclusio
by
cmehta
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AFNI Message Board
3dMEMA - 6 years ago
Hi AFNI experts,
Is there a metric from the output of 3dREMLfit during first-level processing that one could compare across subjects to determine whether the use of mixed effects modeling (via 3dMEMA) is warranted for taking into account variances of contrasts of interest for group analysis? If, in a group, contrast variances are nearly equivalent at every voxel, I'd imagine OLS (via 3dtte
by
cmehta
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AFNI Message Board
Dear AFNI users,
I have a nifti with 200 volumes of spatial maps corresponding to different subjects, along with a design matrix of 200 rows, in the same order as the nifti file, of 10 covariates. Is there functionality for performing something like 3dttest++ using only these files? Basically, I want to perform an ordinary linear regression and only obtain t-stats and p-values for each covariate
by
cmehta
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AFNI Message Board
After a system update, "afni_proc.py" would not run after the "-execute" flag. It would immediately end after generating the TCSH script. After troubleshooting, I found the problem was in setting the zero-padded list of runs .For example, if I have a subject with one run, the line in the TCSH script would be:
set runs = (`count -digits 2 1 1`)
Running "count -digits 2
by
cmehta
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AFNI Message Board
I have a large sample of task-based fMRI's in an event-related design. There was only a single run for each participant. Participants either respond or not respond to a target or foil image. So there are four events I want to model in the GLM for each subject:
1: RT: Response to target
2. RF: Response to foil
3. NT: No response to target
4. NF: No response to foil
For each subje
by
cmehta
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AFNI Message Board
I'm interested in assessing directions of functional connectivity of a 3d+time dataset and a 1D ideal time series in resting state data. For example, 3dfim++ can be used obtain the lag(0) correlations with an ideal file of 200 time points and a 3d+time dataset of 200 subbricks.
Does AFNI offer a tool for obtaining something like 3dfim++ except with cross-correlations obtained at a specif
by
cmehta
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AFNI Message Board
Hi Peter,
Thank you for your suggestions. I followed your recommendations and found some interesting differences in group analysis over children with scans registered to Haskins atlas versus the same group analysis over scans registered to TT-N27. The locations of the significant clusters under the Haskins template align closer with what I would have expected from previous findings (which, to m
by
cmehta
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AFNI Message Board
Hello Pete,
Thank you again for your help; I am following your suggestions and they are helpful.
I wanted to ask you one thing regarding the Haskins atlas. In the first-pass, I performed group analysis on sample ages 8 to 21 all having non-linear registrations to the TT-N27 template.
There after, I identified significant clusters with 3dclust (placed in clust+tlrc). Then I ran whereami of t
by
cmehta
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AFNI Message Board
Thank you Daniel. I'm familiar with the -omask option. However, is there an existing function to use results of the "omask" option of whereami in breaking down 3dclust output (peak voxel, center of mass coordinates, etc) for each cluster? I suppose this might be overkill in terms of reporting results since mapping between significant clusters and ROIs on any atlas are ultimately ap
by
cmehta
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AFNI Message Board
In group analysis, I have found a large cluster of voxels (for cluster-defining threshold, say, P < 0.001) that spans multiple regions of interest under a given atlas (say CA_N27_ML without loss of generality). Running 3dclust can provide information such as coordinates of the peak voxel in the cluster (i.e. highest t-stat or beta).
Is there any AFNI function that directly provides the same
by
cmehta
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AFNI Message Board
Thank you for correcting my misunderstanding of 3dvolreg's function. I misread the afni_proc.py documentation.
Thank you as well for pointing me to @snapshot_volreg. This is an amazing tool! I tried this out on one processed image that was result of linear affine and nonlinear transformations on the same scan.
I ran:
@snapshot_volreg anat_final.SUBJECT_ID_10000000+tlrc \
by
cmehta
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AFNI Message Board
The datasets are from task-based scans. I'm using the afni_proc.py script. In that script, nonlinear registration is indeed performed with 3dQwarp (when inlcuding the -tlrc_NL_warp flag).
Example for nonlinear registration:
afni_proc.py -subj_id ${SID} -script $TCSH_AFNI -out_dir $PWD_TASK \
-dsets $FN_NIFTI \
-blocks tshift align tlrc volreg blur mask scale regre
by
cmehta
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AFNI Message Board
Perusing the AFNI messageboards, I found the idea of using age-specific templates in samples that are not well matched for age.
However, how can one compare across age-specific templates in group analysis? Let's say I want to determine whether a quantitative risk factor explains variation in a sample of 8 to 20 year olds. I used 3dttest++ for group analysis including age, sex, and the ri
by
cmehta
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AFNI Message Board
I do not see major differences in nonlinear vs. linear registrations (to TT_N27), via visual inspection, for a large number of subjects in my sample. Is there an overwhelming preference for using nonlinear registration for group analysis?
Thank you.
by
cmehta
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AFNI Message Board
Suppose I have an errts output with censored TRs. Is there an AFNI function that create a new file with the censored TRs removed?
by
cmehta
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AFNI Message Board
I had initially tried 3dbucket. However, the resultant NIFTI file (after applying 3dAFNItoNIFTI) was not readable by Broccoli:
The exact form of the call to Broccoli was:
# Combining Subject-level nifti files using 3dBucket
[ -f volumes.nii ] && rm volumes*
3dbucket -aglueto volumes sub_1.nii.gz sub_2.nii.gz \
sub_3.nii.gz \
sub_4.nii.gz \
by
cmehta
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AFNI Message Board
I have an error message in running 3dttest++ with flag for Clustsim.
** AFNI version = AFNI_17.0.09 Compile date = Feb 10 2017
** []
** Program Death **
** If you report this crash to the AFNI message board,
** please copy the error messages EXACTLY, and give
** the command line you used to run the program, and
** any other information needed to repeat the problem.
** You may later b
by
cmehta
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AFNI Message Board
I performed subject-level analysis in AFNI for a specific task-based scan, which included standard steps in afni_proc.py such as motion correction, detrending, etc. In step, I also obtained t-statistics for event stimuli. Suppose the t-statistic spatial maps for a stimulus are in a subbrick labeled "stim1" in the stats/REML output file. I wanted to combined the "stim1" subbri
by
cmehta
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AFNI Message Board