Seed Mask
Hello, I am doing a seed to voxel analysis. I would like later to export a mask that include only the Seed itself. Is there is a way of doing it (I would like to do later Intra Class Correlation and...
View ArticleBug report: conn_batch
Line 939: if isfield(batch.Setup.subjects,'descrip'), CONN_x.Setup.l2covariates.descrip{nl2covariates}=batch.Setup.subjects.descrip{neffect}; The last variable, neffect, should be ngroup on this line...
View ArticleRE: Set up error (Any idea on how to fix this?)
Hi All, Ive got a similar problem as this post, however, it seems that my spm is looking for a file i dont have. I am trying to run a preprocessing script from somebody else in my pc and it seems it is...
View ArticleDefining descriptions for L2 covariates (subject effects and groups) - error...
In the excellent 'conn_batch.help.txt' that provides documentation for building CONN batch specification structures, there are two entries for the 'subjects' field (lines 171 - 188), denoting effects...
View ArticleUsing denoising outputs in another project
Hello All, I would like to import the outputs from the denoising step into another project. Is there a recommended way to accomplish this? From, Humza Ahmed
View Articleerror in "Importing functional data" step
Hello, I am doing the First level analysis using my task related functional MRI data set. I did preprocessing using my own pipeline. I have implemented conn analysis successfully using different data...
View Article2nd level voxel-to-voxel group_MVPA interpretation
<font style="vertical-align: inherit;"><font style="vertical-align: inherit;">Hello,</font></font><font style="vertical-align: inherit;"><font style="vertical-align:...
View ArticleIs preprocessing a deterministic process?
Hi Alfonso, I have a question about preprocessing. A year ago, I used my raw nifti data (e.g. ABCD.nii) and I ran the default preprocessing pipeline in CONN. This generated the uABCD (realigned &...
View ArticleAnalysing specific frequency bands
Hello, I am thoroughly enjoying using Conn for my analysis. Thank you for the software! I am interested in decomposing my fMRI time series into different frequency bands and studying connectivity...
View ArticleAdding QC covariates to second level
Hi All, I have used conn to preprocess, denoise, and run first level analyses. The preprocessing / denoising generated the usual second level QC covariates. However, I only see the AllSubject's...
View Article2nd lvl analysis
Hi, I´m comparing two groups (patients and controls) and perform ROI-to-ROI analysis. When choosing "any effect among controls or patients" I have significant values. What I don´t understand is why I...
View ArticleTwo resting state scans -- averaged?
Hi, I have two five-minute resting state scans for each participant. When I put them both into conn, after the preprocessing is complete, I only have 1 rest condition. To confirm, are these scans being...
View ArticleMultiple tests for same groups
Hi Afonso and all, I have a group of subjects (20). I would like to make this group of subjects 4 groups (such that those same 20 subjects are going to be in 4 groups but they differ in something in...
View ArticleError : covariates 2nd level - Index exceeds number of array elements
Dear all, When i try to provide different covariates for 2nd level analysis , i am incurring an error which suggests index exceeds number of array elements I have counted the array index and it exactly...
View ArticleBest approach for pre/post w/ possible perfusion changes?
I would like solicit ideas on what functional connectivity processing methods/corrections might be best when one has pre/post data where the likelihood of perfusion changes over the scan and re-scan...
View ArticleSPM12 prepro batch implementation
Dear Alfonso, We are trying to apply identical preprocessing pipeline of SPM12 (located at "...SPM12\batches\prepro_fmri.m") via CONN. However, at the coregistration stage, CONN doesn't allow us to...
View ArticleWhat is the contrast definition at 2nd level for comparing the Condition A of...
Dear All, We have a study including 1 session for control group and 2 sessions(pre and post treatment) for Patient group. We want to compare functional connectivities (seed to voxel) among those three...
View ArticleCONN Preprocessing error
Hello CONN community, I am currently running my preprocessing step on CONN and kept meeting with this error. [b]Computing mask... : Failed 'Realign & Unwarp'[/b] [b]Matrix dimensions must...
View Articlehow to employ func.gii to perform surface-based FC analysis?
Hi everyone, To conduct surface-based FC analysis, the manual shows that we should enter the T1 or brainmask volumes in the subject-specific mri folder generated by Freesurfer, but it still uses the...
View ArticleError when working with Conditions
Any changes I make in the Conditions results in an error. This happens when I try to create a condition manually, or when I try to import my .txt file. Thanks for any help. [code]ERROR...
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