importing second level covariates
Hello Is it possible to import multiple second level covariates at once from a text file? This function in the CONN gui seems to only allow for the selection of one covariate at a time
View ArticleBOLD Signal Falling to Zero: What On Earth Is Happening Here?
I'm getting a very odd result: when I plot the ROI BOLD series after denoising, I get a very strange artifact: the BOLD signal will sometimes simply drop to 0, without any variation for seemingly...
View ArticleQuestions about Harvard-Oxford Subcortical parcellation used for Conn toolbox
Hello I have some questions regarding the default atlas used in CONN. I am trying to identify certain subcortical structures using the HarvardOxfrod_Subcortical.xml file (attached in this email for...
View ArticleRE: Motion Parameters
Dear Boshra, I would say that you are correct, and that you can either use the 12 parameters from the HCP dataset and remove the derivatives, or use only the 6 parameters without derivatives and then...
View ArticleUsing CONN preprocessed and denoised data to do ICA in GIFT
Dear CONN users, I successfully preprocessed and denoised my resting-state data in CONN. But when I try to import these preprocessed and denoised data (i.e., niftiDATA*_Condition000.nii) to GIFT to run...
View Articledynamic ICA
Hello, I tried to use dynamic ICA but I do not really understand it. (Neither the method nor how to interpret the results given by conn). Are there any tutorials or paper I may read? Best regards, Eli
View ArticleInterpreting the Contrasts for ROI analysis
Dear Conn experts , I am doing ROI-ROI analysis in which i am comparing two groups ( Group A and Group B) , Could you please let me know how to interpret the results of contrast Group A > Group B...
View Articlemultiple datasets per subject
Hello, I have a relatively complex design and I'd really appreciate your inputs on whether I have defined the project correctly. In one fMRI session, I have a 10 minutes resting state pre stimulation,...
View ArticleRE: Cluster extent thresholding of first-level connectivity maps
Dear Stephen, Thank you very much for this exhaustive response! For the voxel-wise correction, I checked a box in CONN set-up options to create first level seed-to-voxel FDR corrected p maps. Then I...
View Articlelow signal intensity issue
Hello! I am running CONN Toolbox and examining connectivity using ROIs. We have signal dropout in an ROI that includes the OFC. I know that you can mask to grey matter in the CONN toolbox, but I was...
View Articleconn model set up
Greetings experts from down under i have run a data set with two time points one year apart in 12 patients and reached to setting up the model. Although i have gone through the previous posts on this...
View Articleare motion regressors overkill with HCP FIX data
My student recently completed an analysis of HCP data using the FIX clean data following the conn_batch_humanconnectomeproject.m script. The script imports the motion regressors, and so conn uses them...
View ArticleCONN crossover analysis
I am struggling to set up a contrast for what appears to be (at least for me) a complex analysis. We have a one year crossover study with two groups: Group one received drug for the first 3 months,...
View ArticleICA versus seed-based analysis
Dear All Dear Alfonso This question is a bit conceptual: what is the compatibility/ the common way of using ICA and seed-based method together? In practical terms, is it justified to take e.g. a...
View ArticleVoxel-toVoxel analysis within a mask
Hi Alfonso, I am interested in running a voxel-to-voxel analysis within a region of interest. Specifically, I'd like to compute the average correlation between a given voxel and the rest of the voxels...
View Articledifferent number of slices in a within subject pre/post design
Hi all, I'm trying to use conn to process some resting state data, and I've run into an issue that I was hoping you might be able to give me some advice on. The study is a within subject placebo...
View Articledecreased temporal SNR after preprocessing and denoising
Hi Alfonso, I preprocessed a resting state fMRI study, pretty much using the defaults (I am attaching the conn_batch script, just in case). Before preprocessing I computed a tSNR of about 96 using...
View ArticleSingle 2nd Level ROI-ROI Analysis with Some Missing ROI's
Hello, I am working with functionally defined ROI's at the individual subject level using 4 different functional localizer scans. As you probably know, when doing this, sometimes an individual won't...
View ArticleRE: Error at 1st level: incorrect # ROIs
Hi Suzanne, Did you ever find a way to resolve this error? I am getting the same error at this exact step. I have tried re-running the denoising step as the prompt suggested, but still receive the...
View ArticleVoxel-to-voxel contrast
Hello all, I'm running a intrinsic connectivity contrast but I get this weird maps (attached). Do you have any tips? Thanks Davide
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