Seed-based analysis finds a cluster within the seed
Dear Alfonso, dear CONN users, I ran an all-CONN-default seed-based analysis that compared resting state before and after treatment. However, one of the significant clusters is within the exact same...
View Article#2 permutation/randomization analysis
In second level analysis, I want to choose #2 permutation/randomization analysis. However, with p < 0.001 p-uncorrected. Can you let me know how to change it? If I go to "advanced Family-Wise Error...
View ArticleError using MATLABbatch system
Hi everyone, I am new to using CONN and I am running a preprocessing using a batch script. however, the error message received was : The following modules did not run: Failed: Realign & Unwarp...
View Articleextract r value between rois in dyn-ICA
Dear Alfonso，  I wonder if conn can extract the r value in the dyn-ICA and what does this r value stand for（the average value of every time series? ). At the same time, if I want to explore the...
View ArticleRE: [BATCH] Secondary dataset functionals_type = 2
Hi Alfonso, Thank you very much for your help! Sorry for the late reply, at the time I found a twisted way to make it work and forgot I had posted this here. Now I am working with the newest version...
View Article2X2 ANOVA interaction with covariate
Dear CONN toolbox experts, I am trying to do a 2x2 anova analysis with a covariate. I have two groups (experimental and control) and two times (pre and post) and I want to see group x time interaction...
View ArticleFlipping image
Dear Expert, My fMRI data, when viewed in SPM, some images have 3x3x4 voxel dimensions and some images have -3x3x4. Should I flip the image so that all images will have same dimensions? If I leave...
View ArticleSecond Level Nuisance Covariates
I am running my first analyses in CONN and I am trying to thoughtfully consider which nuisance covariates to include in the 2nd level group analyses. CONN automatically includes quite a few and I am...
View ArticleRE: Understanding the ICA.timeseries.mat file
[color=#000000]Hi all, [/color] [color=#000000]Wondering if anyone has any thoughts/advice on this? Bhanu [/color][i]Originally posted by b shar:[/i][quote]Hello Conn Community, I'm still somewhat...
View ArticleRE: Error : Reference to non-existent field 'X1'.
Dear Alfonso, Thank you, this took a while (I guess I removed ROI to voxel to save time and disk space) and there are no errors at the moment. It seemed you aimed pretty well! Thanks again, Sincerely,...
View ArticleHow conn deals with non-active voxels inside the brain mask
Hi CONN users! Some of my functional images from some subjects are cut-off at the bottom of the cerebellum (because the scann didn't take the whole brain, including the whole cerebellum), so I was...
View ArticleUnable to display significant values in ROI-ROI connectome ring
Dear all, I am facing an strange problem, when i calculate ROI-ROI effects , in the results i notice positive and negative functional correlation but when i press display results i am not noticing any...
View ArticleExport .surf.nii file to Freesurfer ?
Dear all I have preprocessed fMRI data (200 volumes) in CONN toolbox using resampling on subject's fsurfer surface. Beside analysing surface data in CONN, I would also like to use the .surf.nii file...
View ArticleNumber of voxels in atlas ROIs
Hi there, I performed a seed-to-voxel analysis using ROIs from the Conn atlas as my seed regions. How can I find out the number of voxels in each of the Conn atlas ROIs? I have some reviewers who have...
View ArticlegPPI contrasts and interpretations
Dear all, I'm running a gPPI analysis (seed to voxel) with 2 groups and 3 conditions. I test for the functional connectivity of each group in a condition1>condition2 contrast. There was no...
View ArticleWhat type of inference can be made from a roi-to-roi map with all rois selected
Dear Dr. Alfonso, thank you for your help in the forum. I am wondering what kind of inference can I make if I had no a priori hypothesis and just selected all the ROIS in the brain to a Roi-to-ROi...
View ArticleAbnormal beta value
Dear Alfonso, I have been doing some ROI-to-ROI connectivity analysis and looking at the average effect across all subjects ( I selected bivariate correlation in the first level analysis). I have done...
View ArticleSession design in CONN
Hello Community I am trying to analyse task based connectivity in a 10 patients and subjects. I have 4 sessions and in each session we have 4 conditions. I skipped 2 conditions as those were the...
View ArticleRE: Seed-based analysis finds a cluster within the seed
[color=#000000]Dear Victoire,[/color] [color=#000000]That's perfectly fine, SBC within the seed area is typically interpreted as indicative of the level of regional homogeneity or coherence within that...
View ArticleRE: #2 permutation/randomization analysis
[color=#000000]yes, that is exactly correct[/color] [color=#000000]Alfonso [/color][i]Originally posted by Ho-Ching Yang:[/i][quote]In second level analysis, I want to choose #2...
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