RE: CONN batch scripting: How to skip already-done things?
Thanks for the reply Alfonso. I have a project with ~95 subjects, and the only preprocessing I am using CONN for is functional_art. All other preprocessing is done before import to CONN. So I executed...
View ArticleLarge cluster identified from seed to voxel analysis
Hi, I just ran seed-to-voxel analysis with two groups and selected a roi seed (left angular gyrus( Largest and most significant cluster here is a size of 27969 which seem to cover large part of frontal...
View ArticleRE: Lesion Masks
<h6>Hi Alana, I am trying to execute a masked cost function as well. I found a step wise description...
View ArticleRE: dealing with both surface and volumetric subcortical and cerebellar areas...
Hi, I wanted to ask if there were any changes in the last version to support CIFTI? Or new ways to perform combined surface/volume analyses? Thanks, Rotem
View ArticleRE: Conn17a Networks
Hi all, I just randomly came across this forum. We published in 2018 using these ROIs using a relatively simple ROI-to-ROI analysis. If anyone is interested and needs a reference see Little, 2018...
View ArticleDynamic connectivity error, data will not populate
Hello! I am trying to run a dynamic connectivity analysis, however, when selecting the first level dyn-ica tab in conn, nothing populates and I receive the following error: Index exceeds the number of...
View ArticleICA Spatial Match to template?
Hi Conn Experts A quick question that have been asked before but I've found no substantial answers. I'm wondering what was used to compute the spatial match to template in the ICA tools (ie SPM...
View ArticleError: Index exceeds the number of array elements
I am new to conn. I have a set of data already in mni space. When I ran the "Setup", in the Preprocessing I just chose "functional Label current functional files as "mni-space data" & functional...
View ArticleRE: Realignment & Unwarping fails for some subjects
Hello again, I don't know if this will help or not, but normal realignment (without Fieldmaps) works well for every subject. It's only the Realign and Unwarp that doesn't work (I have done really many...
View Articlefunc.surf.nii denoised files to rh/lh.nii files
Hi, I am conducting surface-based denoising in CONN on the fmriprep r/l.func.gii cleaned files (after converting them to func.surf.nii files). I wanted to ask if it is possible after denoising, to...
View ArticleRE: NifitDATA output file from denoising
Hi Jourdan, As I experienced the same problems as what you described, I wonder if you had resolved the issues. Thanks a lot!
View ArticleSession specific re-alignment
Hi, My main question is, is there a way of specifying in batch preferably (but also in GUI), that you want each session to be realigned intra-session (and not to the first volume of the first session...
View ArticleNII file not recognized in Conn
Hello, I tried loading a NIFTI file to Conn (Set Up), to be used as a seed (binary mask) for future analysis. However, it seems that Conn does not recognize the file at all (attached a relevant...
View ArticleQA - Functional Data Normalization
Hello, Looking through my "QA normalization: functional data + outline of MNI TPM template" output, quite a few of my subjects appear to have issues with the top and bottom most slices, with the bottom...
View ArticleQA information for multiple sessions
Hi, How can I obtain QA plots and images to check registration and normalization of functional and anats for multiple sessions? I am only able to create and view the plots for my session 1 data. Best,...
View ArticleRE: Denoising step disrupts the image with diagonal lines
Help? Please, still stuck ://
View ArticleWhat do the Red and Blue node Stand for
Hello, During 2nd-Level ROI-to-ROI analysis there are some red lines that connect to blue nodes and blue lines that connect to red node. I understand that the red/blue are meant to represent...
View ArticleOutput denoised nifti files
Dear Experts, I have seen in an earlier post from Alfonso that the denoised functional timeseries data should appear in the "conn*/results/preprocessing/" folder as...
View ArticleReorienting Scans
Hello, I am attempting to integrate a harmonization step (to control for site effects). I preprocessed the files and ran it through our harmonization script. However, when these harmonized files are...
View ArticleAdding Enabled Analyses to Project
Hi fellow CONN users and CONN developers, I have what I believe is a fairly straight forward question for which I can't seem to find a clear answer. I've completed analyses of a project using...
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