RE: Multi-session pre-post design QC_ValidScans for each separate session
[i]If you prefer instead to compute QC_ValidScans directly you may do so by using in step 2 above the following options instead:[/i] [i]consider covariate scrubbing: raw values[/i]...
View ArticleSecond-level Seed-to-voxel analysis interpretation
Greetings, I am currently conducting a Seed-to-voxel analysis of connectivity between six seeds (left ACC (x,y,z = -6, 18, 21), left orbitofrontal cortex (OFC; x,y,z = -42, 24, -6), right insula...
View ArticleQA as a variable in the second-level analysis
Hello, After all preprocessing steps (with SPM Art Toolbox as well) I have 6 additional Quality Assurance variables as second-level covariates (QA: white matter, grey matter and csf: vol and eroded)....
View ArticleAdding subjects
Dear Alfonso, when I add new subjects to an existing dataset the GUI shows not an empty subject for the newly created but copies the last from the previous dataset. Is this only a graphical issue or is...
View ArticleError while importing ROI data
ERROR DESCRIPTION: Error using rex>rex_do (line 741) mismatched number of scans and covariate datapoints ([2 1] vs. [800 16]) Error in rex (line 180)...
View ArticleError importing results to CONN project
2019-Mar-07 17:50 : Preparing functional Label current functional files as part of list of Secondary Datasets ("original data" label) Performing functional Label current functional files as part of...
View ArticleRE: Extremely high values of contrast estimates in SPM after using CONN...
[color=#000000]Hi Alfonso,[/color] [color=#000000]The Global Normalization is already set to "None" in spm first level. [/color] [color=#000000]Attached is the image of the same. [/color]...
View ArticleCerebellum Cut Off after Preprocessing
Dear Experts, I imported both structural and functional images for 30 subjects and preprocessed them on CONN using default pipeline. When I check the images after preprocessing, I realized a lower...
View ArticleCONN 18b frozen when setting the preprocesing steps
Dear Conn Users, I used CONN version 17a, then 17f as SPM12 toolboxes running under Matlab R2017b on a Linux machine. Everything was running properly for a while but recently, everything I process in...
View Articledenoising (compcor) is shifting all correlation histogram means to zero
We are preprocessing data using other methods, but then put the timeseries into CONN so we can do compcor on them and subsequent analysis. I'm attaching a screenshot from the QA of histograms before...
View ArticleExtracting fMRI data after denoising step
Hello everybody, I'm using CONN to preprocess rs-fMRI data and am especcially interested in the denoising functionality. Is it possible to save the denoised fMRI data so that I can use them outside of...
View ArticleDifferent numbers of runs in fMRI task
Dear Alfonso, After preprocessing our fMRI task with a standard pipeline, we also applied ICA AROMA to each run of the task (6 runs in total). For some subjects, we had to remove some runs, meaning...
View ArticleProblems preprocessing imported data unwarped with fsl topup
Hello, I am trying to perform preprocessing of resting state data (with conn 18b) after performing motion correction and unwarping with fsl mcflirt and topup, respectively. I have imported the motion...
View ArticleRE: CONN 18b frozen when setting the preprocesing steps
[color=#000000]Dear Larra,[/color] [color=#000000]Could please clarify what you mean by frozen? (the window is unresponsive? it throws error messages when you attempt to interact with it? can you...
View ArticleDenoising: dimensions for WM and CSF
Dear Alfonso, 1. I am using the Conn 17. In the denoising tab, I had input the number of dimensions for White Matter(5) and CSF(5) under the 'Confounds' field. Am I correct to say that by default, 16...
View ArticleROIs for ALFF
Dear all, I want to analyze simple resting state (ALFF/fALFF). Is it possible to replace the CONN internal brain template by a template containing only the brain regions of interest? Can there be...
View ArticleRE: BACTH Processing Help
Thanks Alfonso! The matlab version I'm using is '9.2.0.556344 (R2017a)' and I'm now on CONN18b. I'm still getting this error and I can't seem to figure it out: Error using cell/strmatch (line 19)...
View ArticleRE: denoising (compcor) is shifting all correlation histogram means to zero
Alfonso, Thank you for your reply. The WM and CSF masks look ok to us. In any case, we are importing data to CONN that are in MNI space, and the WM/CSF masks are those in CONN (also MNI space)....
View ArticleICA networks processing does not run
Dear colleagues, I am using the Conn GUI and everything is running except with the ICA networks part (left icon on RESULTs (2nd-level). When I tried to run it I get the attached message. Basically It...
View ArticleProblem with non-parametric cluster-level statistics (permutation tests)
Hi Alfonso, I am running a surface-based functional connectivity analysis with conn and it is going well until the permutation tests for second level analysis. It always froze on the interface...
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