RE: questions about removal of first scans
Thanks for your detailed explanation, your work is amazing. Best Weng Xin
View ArticleDiscrepancy between results viewer in Conn, and SPM 12, within-network...
Hello all, I recently did an ICA analysis, comparing the effects of drug vs placebo on various resting state networks. When I load the results viewer, I see the hypothesized difference between my...
View ArticleDot indexing error in BATCH
To whom it may concern, I am writing a script in MATLAB to run an analysis in CONN toolbox, using BATCH commands. In there, I set up some commands to do the appropriate preprocessing steps:...
View ArticleConsidering mean and maximum motion
Dear Expert, I need your help for removal of a subject, particularly sub-11. Maximum motion shows 9.2 where as mean motion is within the 3rd Q + 1.5 IQR and and 1st Q + 1.5 IQR. Please have a look on...
View ArticleBATCH unrecognized option done.
To whom it may concern, In my script to run a CONN analysis, I am trying to make it do a certain sequence of preprocessing steps, using the following script:...
View ArticleImporting fMRIPrep-20.0.0 ROI masks
Hi Alfonso, I was watching the log files as I was importing a dataset I processed this week. At the point of importing the structural images and ROIs, ROIs 1, 2, and 3 are imported as...
View ArticleConjunction analysis in CONN
Dear CONN, I have one group, 4 conditions and I am performing a ROI-ROI analysis. I want to perform a conjunction analysis: to find those common connections that remain significant in A>D AND C>D...
View ArticleRE: 2x2 ANOVA setup
[color=#000000]Hi Amy,[/color] CONN will use T-stats for ANOVAs with two levels for each factor and F-stats for ANOVAs with three or more levels (for details about GLM stats see...
View ArticleViewing output/results from 1-st level and 2-nd level Analysis using CONN's...
Hi CONN Community, I have done all the analysis I need with CONN batch command line but I am having trouble with viewing or visualizing the results (both 1st and 2nd level). All the tutorials and...
View ArticleRE: denoising output
Dear Alfonso, Thank you so much for this answer! It worked great. I have another question- we want to stay in the subject volumetric space (not a surface). Our preprocessing output has a u*.nii file...
View ArticlegPPI with sparse temporal sampling
Hello Alfonso, I have a task-fMRI experiment applying sparse temporal sampling (TR = 9 s, scanning time of a volume = 2 s). I want to do gPPI by CONN. I don' t know whether some options or parameters...
View ArticleResult interpretation
I have gotten result. Blue in color connection is interpreted as anti-correlation. If it Is anti-correlation, does it means negative connectivity? Negative correlation is by means hypoactivation for...
View ArticleMultiband sequence / subsecond TRs
Good afternoon everyone, I'm about to run several analyses of fMRI data that was acquired with multiband sequences. The TR was shorter than 1 second in all cases (0.7 / 0.8 sec). While the advantages...
View ArticleGlobal correlation restricted to positive correlation
Dear CONN users I would like to restrict a voxel-to-voxel analysis to positive correlation above a certain threshold (e.g. r>0.2). Does anybody know how to do that? Thank you very much Hannes
View ArticleQuestion about "Demeaning & Detrending" strategy as identified...
Hello all, As I'm working on the preprocessing/denoising methods of my paper, I came across a term that I'm unfamiliar with and very little leads as to what it means. In two recent denoising strategies...
View ArticleMVPA with behavioral measure
Hi all, I would like to use a data-driven whole brain approach (i.e. MVPA) to find which regions of the brain correlate with a behavioral measure undergone outside the scanner. I have got two groups of...
View ArticleROI-ROI fucntional connectivity matrix not symmetric
Hello, I have been using the result of first level analysis (GLM, bivariate correlation, ROI-ROI, hrf weight) as the weighted connectivity matrix between ROIs for further functional connectivity...
View ArticleCONN compatible with HCP MSM-All CIFTI data?
Hi all, I searched the forum but I only found two (unanswered) threads asking about the compatibility of the CONN toolbox with CIFTI data. Is CONN compatible with CIFTI-formatted fMRI inputs? I would...
View ArticleRE: denoising output
Dear Inbar, [color=#000000]Yes, that resampling is likely due to your choice of '[i]analysis space[/i]' (this is defined in [i]Setup.Options[/i]). The default option there is "[i]Volume: same as mask...
View ArticleRE: Event-related conditions with batch
[color=#000000]Hi Kaitlin,[/color] [color=#000000]Yes, the 1-contrast-only issue should be fixed by changing the line:[/color] for Con=1:length(nconditions) [color=#000000]to:[/color] for...
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