Modeling stable status -- 3 TRs no variance across ROIs?
Hello, I de-noised my rs-FMRI data in CONN and for a particular analysis I am conducting I checked variance across 170 brain regions for each TR. See image attached. It's clear that no subject has any...
View Articlevdm creation and 2nd-level results
Hello, I have a question about one of the pre-processing steps in CONN toolbox that involves "creation of vdm for susceptibility distortion". It appears that this step only accepts double-echo fieldmap...
View ArticleHow to add respiration & cardiac data in setup
Dear all, I know I should add my physiological data in setup step in CONN, and then use RETROICOR regressor to clean my data, however I cannot find any help in CONN web-page/manual. My respiration and...
View Articlebatch setup.outputfiles resets
Dear Alfonso, I am currently trying to run a batch script using Andy's code + the batch that I saved from my conn project. It is working perfectly so far, except for one problem- I need the denoising...
View ArticleUse of ICC and ILC
Dear Alfonso, dear all Apologies when this question sounds trivial. Still relatively little has been published on ICC (Intrinsic Connectivity Contrast) and ILC (Integrated Local Correlation) and I...
View ArticleDifferent 1st level analysis with additional subjects
Hi everyone, I am trying to do preprocessing and 1st level analysis of some resting state fMRI data. The data has been preprocessed with SPM and I am only doing ART outlier detection and denoising in...
View ArticleRE: Voxel-to-voxel: unequal voxels when combing datasets
Hi Alfonso, Thank you so much, this seems to have done the trick!! Best, Kaija [i]Originally posted by Alfonso Nieto-Castanon:[/i][quote][color=#000000]Hi Kaija,[/color] Not exactly. Since group-ICA is...
View ArticleHow to specify custom subject IDs for CONN to use in output filenames?
Hello, I am new to fMRI processing and have set up a CONN batch script to process data across multiple ABIDE sites. As inside conn/results/preprocessing, the names are stored as...
View ArticleRE: Combining several resting statescans into one session
[color=#000000]Hi Alfonso,[/color] [color=#000000]could you please clarify whether this is normal or not?[/color] [color=#000000]Thanks,[/color] [color=#000000]Best,[/color] [color=#000000]Amy[/color]...
View ArticleRE: Output space: Anatomical scan
Hi Alfonso, In addition to the T1 anatomical space I mentioned earlier in this thread, I also tried to perform the fMRI processing analysis in the subject's native diffusion space. In order to do that,...
View ArticleRE: “Case weights”
[color=#000000]Hi Mayron,[/color] [color=#000000]That's an interesting question but unfortunately no, CONN does not have any general way to specify different participant-level weights that could be...
View ArticleVoxel-wise time series extraction
Hello all, I have just started using Conn and wanting to get familiar with it.. I have pre-processed my fMRI data in SPM and want to extract the voxel-wise BOLD time-series in Conn for all my...
View ArticleDenoising step methodological doubt
hi Alfonso and the whole community. I'm conducting a connectivity study during task. Specifically I am carrying out a functional connectivity (weighted GLM) with hrf weighting analysis using...
View Articlecreatemniroi() func with 264 coordinates returns nii file with...
Hello everyone. I want to create a .nii file for 4mm radius spherical ROIs based on 264 coordinates. The coordinates of MNI space come from Power et. al. 2011 and are stored in ROI_coords.txt file. I...
View Articleatlas.nii in CONN does not match fmriprep preprocessed T1
Dear Alfonso, I did preprocessing in fmriprep, and then imported fmriprep output into CONN. I found the dimension of atlas.nii is different from that of fmriprep output. The Harvard-Oxford atlas.nii...
View ArticleWhy connection colors are blue?
Dear Conn Users, I have two groups and two conditions for task fMRI. I have selected two groups and two conditions with the between-subjects contrast [1 -1] and between condition contrast [1 -1]....
View ArticleCONN preprocessing error
Dear Alfonso, I am trying to use CONN 18b with SPM8 to preprocess data for 3 subjects (1 session). However, I keep getting an error. I am using the default preprocessing pipeline for volume-based...
View ArticleRE: Correct *Across ICNs* for Multiple Comparisons
Hi Alfonso, Is there a need to correct for multiple comparisons when you are investigating multiple behavioral variables? Ie - I am selecting one behavioral subscale at a time (that is part of a larger...
View ArticleUsing a new atlas in CONN
Dear Alfonso, Thank you for such a great toolbox... I am using CONN to understand dynamic functional connectivity.. But in my analysis, I do not want to use the default atlas/ROIs in my analysis......
View ArticleRE: How to import the Yeo 7 Network to Conn in surface-based pipeline
I have the same question. I am wishing to do a surface-based ROI to ROI analysis with the Yeo atlas. I have downloaded the Yeo atlas folder from the Freesurfer website. Can anyone provide insight into...
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