RE: Viewing output/results from 1-st level and 2-nd level Analysis using...
[color=#000000]Hi Jason,[/color] [color=#000000]You may simply use the syntax:[/color] [color=#000000] conn_display /myresultsfolder/SPM.mat[/color] [color=#000000]to view your second-level results....
View ArticleRE: Using denoising outputs in another project
Hello Alfonso, I am running into some storage limitations. Is it possible to do any of the following: 1. Use the denoised DATA files in /preprocessed directly without the setup step for a new project....
View ArticleConn_batch_humanconnectomeproject
Hi all, i'd like to use the Conn_batch_humanconnectomeproject to analyze HCP fmri data. I am working on a linux ssh using the connstandalone linux. Is there anyway to use this script provided in this...
View ArticleError while running surface based preprocessing using freesurfer data
Dear Alfonso I want to extract functional connectivity of my data in subject space, using the surface based ROIs from freesurfer. I have imported functional data along with T1.mgz and gm,wm,csf from...
View ArticleRE: including a parametric modulator
Hi Alfonso! I hope you have been doing well (and staying healthy!). I am running a parametric modulation analysis in conn, using the recommendations in this thread. I have one question: it seems that...
View ArticleRE: Lesion Masks
Hi Alfonso, I am interested in your previous answers about incorporating lesion masks in CONN. Where can I find the option labeled 'use default Tissue Probability Map'? In the Preprocessing GUI, I...
View Articleuse default Tissue Probability Map option
Hi Alfonso, I am interested in incorporating lesion masks in CONN. Where can I find the option labeled 'use default Tissue Probability Map' that you mentioned in previous topics? In the Preprocessing...
View Articleerror during Step 5/7: Importing ROI Data
Hello, During the import of the ROI data (before seeing the denoting gui) I have this error: Error using conn_process (line 760) No suprathreshold voxels in ROI file...
View ArticleNew Pre-processing steps
I noticed in the conn pre-processing pipeline, there are a few new steps that have to do with "labelling current functional files as part of a list of secondary datasets". What does this do, and if I...
View ArticleRE: Analysis mask (binary explicit) for limited field of view high-res data
Dear Alfonso, Thank you for this. I am curious if CONN can accommodate some kind of probabilistic mask for analyses, like the one attached. The white areas show where 100% of participants have voxels,...
View ArticleRE: Correction for global signal
Hello, On the CONN website, it indicates that GSR can be completed by "simply defining a new ROI encompassing the entire brain (e.g. a subject-specific brain mask resulting from the outlier detection...
View ArticleInterpretation of second level analysis
Hello, I would like to examine the effect of age on functional connectivity within a specific brain network. I have created the second level covariates 'Control' and 'AgeControl'. Then, in the second...
View Articleinteraction group x condition
Dear Conn-Team, I have a 2x2 Design, meaning two groups with two sessions/condition (treatment vs placebo) I am interested in the interaction of group and condition. How would that look like? From the...
View ArticlefMRIprep import no realignment and scrubbing confounds
Dear all, I have preprocessed my resting-state fMRI data with the fMRIprep pipeline and I am now trying to import these data into conn for denoising and analyzing them. The import works well for the...
View ArticleRE: Event-related conditions with batch
Hi Alfonso, Never mind, I figured it out! I changed the code to: functionalz=cellstr(conn_dir('4D_uaf*.nii')); functionalz=reshape(functionalz,[nsessions,nsubjects]);...
View ArticleResting State Analysis with Downsampled Subject Cortex
Dear CONN community, I have a downsampled subject specific cortex file (15002 vertices) produced from the MEG/EEG software Brainstorm. I would like to use this specific cortex to do fMRI functional...
View Article2nd level analysis group level mask used for analysis
Good afternoon, I had some questions regarding implicit and explicit masks for 2nd level analyses 1. Is there a way to look at the resultant mask used in the 2nd level analyses (both for MVPA and...
View ArticleRE: Multiband sequence / subsecond TRs
Dear Alfonso, Many thanks for your helfpul answer! We have one last question, regarding the use of a multiband sequence for an fMRI study using a rapid event-related paradigm. We are trying to use the...
View ArticleRE: Graph theory in conn
Hi, Alfonso, it is able to perform graph theory analisis in dynamic factors? (doesnt appear at GUI, conn 19c) Thanks
View ArticleRE: Importing fMRIPrep-20.0.0 ROI masks
[color=#000000]Hi Alfonso,[/color] [color=#000000]One last question for the time being (I hope). I am planning to use the default CONN ROI atlas, at least for the time being. I know that in the...
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