Doing an Omnibus Test
I'm fairly new to analysis and this is my first project, forgive me if my question is redundant. I tried to look for answers in the forum, but many answers were specific to resting state MRI or...
View ArticleRE: use smoothed data for ALFF analysis
Just to answer further now that I also used the CONN preprocessing pipeline (which is the one that generates swua*.nii files) ;-) These files are before bandpass filtering, the filter being only...
View ArticleBand-pass filter before denoising (to use rshrf toolbox)
Dear Alfonso, dear CONN users, I would like to use the rshrf toolbox to deconvolve the haemodynamic response function: https://github.com/compneuro-da/rsHRF Unfortunately, it requires a bandpass filter...
View ArticleRE: Examining carryover/order effects in a cross-over design
Dear all, Given that I have a carryover effect in some of my seeds - I decided to add a 2nd-level covariate that accounts for order: it codes 1 for each participant that had the real treatment...
View ArticleFiles created after preprocessing
Hi, I am using Conn toolbox for the very first time and I run into problem after the step of preprocessing. As far as I understand the files created should be named something like "cT1w:3D_TRA" or...
View ArticleRE: Preprocessing error for subject fMRI timeseries during ART outlier...
[i]Originally posted by Tien Nguyen:[/i][quote]Hi, Were you ever able to solve this error? I've been getting the exact same error for one of my projects while my other project using different subjects...
View Article2nd level: contrasts definition
Hello, I am studying the effect of different coviariates (score1, score2) on different seeds (seed1 seed2), on a seed to voxels analysis (usually I use an uncorrected p-value for the height of the...
View ArticleExtracting Beta values from specific coordinates
Hi Conn users and Alfonso, In my second level results, I used a two group contrast (Healthy Controls vs CTS) at baseline. There were a few clusters with increased FC in CTS compared to HC, each...
View ArticleRE: Lesion Masks
[color=#000000]Dear all,[/color] [color=#000000]How could I modify the TPM.nii file? Should I add a new 3D image to the TPM.nii file with the lesion masks of all my subjects?[/color]...
View ArticleCorrelation
To whom it may concern, I have two questions; First, how do I find/calculate an "R-value"/correlation value between ROIs? And how do I choose each ROIs to have that specific r-values? Second, I wich...
View ArticleIs it possible to skip some CONN preprocessing steps
Hi, I've been running one of the default preprocessing pipelines in CONN from the GUI but it crashed on step 6/7 due to a full disk issue. Is it possible to get CONN to skip the first 5 steps and...
View ArticleRE: Potential bugs in preprocessing pipeline
[color=#000000]Dear Dr. Alfonso,[/color] [color=#000000]Apologies for not having reverted back sooner. I am sharing a document that has the slice order for a Philips MRI machine via email. [/color]...
View ArticleQA histogram "bug"
Hi all, This does not apply to most projects but... Starting in version 18.a (or perhaps 17.f), it appears that the before and after denoising histograms of voxelwise connectivity are generated based...
View ArticleICA network (intermediate steps and results files)
Dear CONN community and Alfonso, Excellent work and very friendly interface. Saved a lot timefor fMRI beginners like me. I have a few questions regarding ICA analysis in CONN. I am trying to understand...
View ArticleRE: CONN not reading txt associated with ROIs
Hello Alfonso, Related question similar to Ami's previos question. I'm trying to load the Shen et al. atlas containing 268 parcellations (nodes) in Conn 18.a. I've attached the .csv that accompanied...
View ArticleWaiting for your reply: exporting BOLD denoised timeseries for dynFC
Dear CONN experts, I´m writing to you once more since my question is still unresolved and I have seen some activity in the forum. I would really appreciate if someone could help me clarify this issue....
View ArticleMixed ANOVA interaction - contrasts vectors for 2nd level
Hello, My study design: * 3 groups of treatment (between subjects). * Each group underwent 2 separate sessions (Pre and Post treatment). * Each session contains two conditions ("Baseline" block and...
View ArticleRE: Extracting Beta values from specific coordinates
[color=#000000]Hi Alfonso,[/color] [color=#000000]Do you (or anyone else) have any recommendations?[/color] [color=#000000]Best,[/color] [color=#000000]- Harris [/color][i]Originally posted by...
View ArticleTask-based parameters during denoising/setup
Hi, I am new to CONN and I'm trying to run task-based FC analyses. I have read elsewhere that a high pass band filter around [0.008 Inf] would be appropriate for this kind of analysis...
View ArticleCorrectly add aseg to batch and including extra covariates in denoising
Hi, I'm having trouble turning a gui job into a batch job correctly. In the GUI, whenever you add a structural image from freesurfer, it automatically asks if you want to import the aseg.mgz file and...
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