RE: Conn for fast event designs
Hello Alfonso! In your previous message in this thread you wrote, "These analyses handle the overlap between conditions by entering all conditions simultaneously into a combined general linear model...
View ArticleRE: Mixed effects model for repeated subjects?
[color=#000000]Hi all, I would like to try to bump this again. I am working on a script where many, but not all, subjects have multiple sessions, across different levels of a factor. So I am preparing...
View Articleconditions setup issue
Im working on a batch processing command (below), and am running into an error having to do with setting up the conditions:"testIndex exceeds the number of array elements (2). Error in conn_batch (line...
View ArticleRE: post-hoc analyses using additional software
Hi Alfonso, Thank you for your response - this was very helpful for our analyses. We are now interested in performing a similar approach but this time for an ROI-to-ROI analysis. Within the...
View ArticleRE: Interpretation of [.5 .5] subject contrast results
[color=#000000]Hi Vera,[/color] When defining a model that includes only two groups as subject-effects (e.g. GroupA, and GroupB), and entering a between-subjects contrast [.5 .5], the results relate to...
View ArticleMore stringent thresholding
Hi Alfonso, Hopefully this question makes sense - I've been working with ROI to ROI results from a gPPI analysis recently after contrasting two conditions. The results I've been working with come from...
View ArticleRE: Interpreting scrubbing matrix
Thank you for the response! I have one remaining follow-up question. I was able to produce the dwau*.nii files, and would like to use them to conduct first and second level analyses. However, after...
View ArticleRepeated measures 3 x 2 ANOVA: interaction and main effects contrasts
Dear Alfonso, I hope you are doing well. I have a 3 (pre, during, post treatment) x 2 (real, placebo treatment) repeated measures ANOVA and I am not sure which contrasts to enter in the 2nd level...
View ArticleRE: Continuous subject-level covariate of interest
Hi Alfonso, I'm working with Rany on this project and I had a follow-up question. I have computed the first level analysis using our SC covariate as the interaction factor, in the temporal modulation...
View Articlefmriprep to conn approach
Hi, I'm working on a pipeline for taking resting state data through fmriprep and then into CONN for smoothing and denoising. Rather than importing as an fmriprep file, I've found it easier to just...
View ArticleMVPA analysis
I am trying to run an MVPA analysis and after I run the first level, I am looking at the summary tab at the second level. I am not getting coverage of more than 30% of the voxels according to the graph...
View ArticleSecond level analysis error: Value should be a finite number greater than 0
Hi All, I have a multivariate resting state analysis of about 200 subjects divided into control and diagnosed male/female groups (four covariate files with 0 and 1 to indicate members of each group)....
View ArticleRE: what is the " normalization" in ALLF or LCOR?
[i]Originally posted by Alfonso Nieto-Castanon:[/i][quote][color=#000000]Hi Kim,[/color] [color=#000000]The 'normalization' option in any voxel-to-voxel first-level analysis refers to an optional...
View Articlelinux standalone instalation problem
Hello, I've been trying to install the CONN toolbox using the pre-compiled standalone release, but have been encountering some errors. I'm running on Ubuntu 20.04, which might be a source of problems?...
View ArticlePartly removed data after denoising
Dear all, I am working with CONN for a longer time now. Now I stumbled over a problem in my data which was preprocessed with CONN: preproc_STEPS = {'functional_art' ... 'functional_center' ......
View ArticleGroups creation
Hello community, I have been working with conn scripting for few weeks now and now I wanna do group level analysis through scripts. There are two sets of data namely Alzheimer's (AD) and control...
View ArticleRE: More stringent thresholding
[color=#000000]Hi Kylie,[/color] [color=#000000]Yes, that is perfectly correct, in TFCE analyses you may go to advanced FWE settings and change the default p-FWE<.05 threshold to a more conservative...
View ArticleRE: Interpreting scrubbing matrix
[color=#000000]Hi Mikey,[/color] [color=#000000]There is no need to update the functional files after denoising. CONN automatically saves within your conn project the denoised data using its own...
View ArticleRE: Continuous subject-level covariate of interest
[color=#000000]Hi Grace,[/color] [color=#000000]The "temporal association between connectivity strength and skin conductance" for two ROIs refers, generally speaking, to the correlation between the SC...
View ArticleConn_batch.m typical terminal output
Hi! I just wanted to check whether or not this script was running correctly. I have used the conn_batch_humanconnectomeproject pre-made script here and set it up to run on our severs. It is now over...
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