Dynamic functional connectivity
Hello, May I know the dynamic functional connectivity parameters of CONN? Is it based on sliding window approach or auto-regressive model based? Thank you Madu
View ArticleaCompCor: where to find the PCA results?
Dear, I have preprocessed my fMRI data using the conn toolbox. I am doing both task-related functional connectivity and classic GLM fMRI analyses. For the classical GLM analyses, I would like to...
View ArticleExclude lesions from FC Analysis
Hello everybody, I have a tumour patient to who i would like to do FC analysis. In order to do this I would like to exclude tumour from analysis. I created a mask (.nii image containing only the...
View ArticleRE: Preprocessing (Denoising) Error
Hi Drew, I have run in the samen error when loading my project file or trying to save a project file. Did you figure out how to fix this? Or does anyone else have any suggestions? Thanks! Julia
View ArticleNii files for MELODIC
Hi CONN experts, I wanted to use my preprocessed and denoised files for MELODIC ICA in FSL. Are these the nii's in the results/preprocessing/ folder with the prefix 'niftiNORMS'. If not where can I...
View ArticleSelect “mask with grey matter” and "subject-specific ROI"?
I am inputting a probabilisitic MNI-space left amygdala .nii mask in the set-up phase and am curious if it would be helpful to also mask that small volume using "Select "mask with grey matter" on...
View ArticleRE: How to define "site" as covariate
Hi, I am also looking for answer on how to properly control for multiple sites in the contrast manager. Currently I have 5 sites and have dummy coded them as 5 separate variables. If I want to do an...
View Articlecompcor command line?
Hi -- is there a way to run compcor from the command line on (already preprocessed) functional images? Cheers, Reece
View ArticleQuestion regarding setup and extraction of ROI data
Dear Experts I have a quick question regarding the setup of ROI data. I finished a connectivity-analysis and now want to change a few things, such as masking my individual ROIs with individual grey...
View ArticleWhat mask is used for voxel-to-voxel analyses in SPM 12?
Dear Alfonso, dear all, what mask exactly is used during calculation of voxel-to-voxel measures such as fALFF when using SPM 12? If I understood correctly it used to be the SPM apriori/grey.nii mask...
View ArticleRE: F-test in second-level results
Hey Lihong, For your F-tests, looking at the overall significance of IFG tri or Seed networks.Language.IFG, the significant p-value indicates that at least one connection is significantly related to...
View ArticleMerging pending jobs
Dear Alfonso and other CONN users, I am having difficulty with conn v18.a I have amended the setup of my experiment by adding some additional ROIs. There was initially an error when i tried to progress...
View Articlethe Input image for preprocessing
Dear Professor, I am a post doc in China Sichuan University but a very new beginner of the Conn. Now I have come up with some problems of the input images. I only have the raw structural image and raw...
View ArticleSummarize 1st-level covariate realignment/scrubbing: Parameters
Dear CONN experts I would like to compute a subject-level measures of realignment/scrubbing levels and use these as covariates in the second-level analysis. (seed-based rsfMRI analysis) How do I select...
View ArticleRE: Motion measure AFTER scrubbing
Dear CONN users, I am also interested in the motion measures after scrubbing is done. I followed the steps but reached this MATLAB error: cov = conn_module('get','Setup.l1covariates'); idx =...
View ArticleFunctional connectivity block design: question on conditions and denoising
Dear experts, We performed 3 block-design fMRI runs with during each run - 3 blocks of 18s with muscle vibration at 60 Hz (Cond60) - 3 blocks of 18s with muscle vibration at 20 Hz (Cond20) - 6 blocks...
View ArticleCalculate framewise displacement Jenkinson
Dear Alfonso, dear all, is there an easy way to compute FD Jenkinson using the first level realignment covariate for use as a 2nd level covariate in CONN? Thank you! Best wishes Julian
View ArticleHave to CTRL+C in matlab window to continue ART in preprocessing?
Hello, When the ART toolbox is being called from CONN, I have to Ctrl+C in the matlab window after the files are saved for each subject in order to continue to the next subject. Else the processes idle...
View ArticleIs small cluster size problematic?
Hi, I have run some second-level seed-to-voxel analysis in conn. My model is quite simple: I am using multiple regression to find the voxels whose connectivity with a few ROI seed regions correlate...
View ArticleWhere are details regarding ART settings recorded
Dear Alfonso and other CONN users, Hopefully a simple question - where are details regarding one's chosen ART settings recorded in the CONN_x file? It appears some files have a CONN_x.SetupPreproc.log...
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