Masking out the cerebellum?
Hi, I have preprocessed 64 subjects using the CONN default preprocessing pipeline. The lower part of cerebellum has been cut off in the QA normalisation with MNI boundary. (see attached) When I...
View ArticleRE: Error message - Reference to non-existent field 'X1'.
Hi Alfonso, Thanks a lot for your response! When I checked the logfile.txt, I found Step 4/7 of Setup pipeline was skipped. Hence, I am wondering the possible issue is that the seed-to-voxel analysis...
View ArticleRealignment & Unwarping fails for some subjects
Hi Alfonso and everyone, I am having a problem with the Realignment and Unwarping preprocessing step when fieldmaps are available. To keep it short, in some subjects, this step fails and produces bad...
View ArticleHow to use "QA_InvalidScans" as covariate in second-level analysis
Dear CONN experts, I am using CONN version 20.b and have read in the manual that it is possible to use "QA_InvalidScans" as a covariate in the second-level analysis. Unfortunately, it is not clear to...
View ArticleDenoising doubt
Hello Alfonso. I am currently working with a sample of stroke patients. Reviewing the literature I have seen a method to regress the lesion-linked signal (https://doi.org/10.1016/j.nicl.2017.10.027)....
View ArticleScrubbing / Denoising Issue
Hi Everyone, I am conducting my second project with the CONN toolbox. I am working with a cross-sectional group (n = 105; 1 MRI session) of older adults with MCI. For context, I am using version 20.b...
View ArticleDenoising step disrupts the image with diagonal lines
Hey Alfonso! I would love for your help. I am currently running pre-processing with the steps bellow, and outputting the denoising image (the previous step was realignment). I did this for previous...
View ArticleQA information for multiple sessions
Hi, How can I obtain QA plots and images to check registration and normalization of functional and anats for multiple sessions? I am only able to create and view the plots for my session 1 data. Best,...
View ArticleMVPA Contrast Stats
Hi Alfonso, I hope this finds you well. What is going on "behind-the-scenes" in my MVPA voxel-to-voxel analysis when I set: Subject effects - "All Subjects," "Age," "Sex," "MeanMotion," "Group,"...
View ArticleRE: Cluster computing - SLURM jobmanager test fails
Hi Alfonso, You are correct that the test does not progress, or show the second line 'Waiting for grid/cluster jobs to finish'. As for the suggested tests:>> conn_jobmanager options cmd_submit...
View ArticleRE: ROI-to-ROI Connectivity Line Color / Ball Mismatch?
Thanks, Alfonso. This helped for the 2D visualization, but the issue still persists for the "display 3D" option. Is there code that can be altered to make the display 3D also reflect Allsubjects and...
View ArticleRE: Graph theory in conn
Hi Alfonso Can I add my own correlation matrices to the toolbox for graph analysis? Thanks
View ArticleRE: FC analysis of already preprocessed data
Hello Maximilian, Were you able to solve this issue? I'm having the same problema and not finding any answers! How did you work around this? Thanks in advance, Miguel
View ArticleDynamic connectivity Error
Hello! I am trying to run a dynamic connectivity analysis, however, when selecting the first level dyn-ica tab in conn, nothing populates and I receive the following error: Index exceeds the number of...
View ArticlePotentially Corrupted File
Hello, I recently added new ROIs to an already existing project, and have been trying to process all subjects through first-level for those new ROIs so that I may extract RRC matrices. When I get to...
View ArticleRE: Scrubbing / Denoising Issue
For anyone interested, I figured this out: 1) I exported second level covariates (i.e., max motion, mean motion, etc.) to SPSS and identified extreme outliers via boxplots 2) I did the same thing...
View ArticleProblem using CONN: single group rsfMRI & 2*2 within-subjects behavioural...
Dear CONN experts, Hi. I am a beginner in this field. And I encountered a problem. I have one group subjects who completed rsfMRI and behavioural experiment separately. Behavioural experiment included...
View ArticleFailed merging after parallel jobs - can't visualise results
Dear Conn experts, I tried running 6 parallel jobs for preprocessing pipeline. It worked for 4 of them, and 2 failed. I clicked on the restart button for the 2 failed jobs and they successfully...
View Articlehow to change the reference brain for display?
Hi! Under ROI second level main results (ring or matriix) display, the results are automatically overlaid on a reference brain/glassbrain (pic attached), which I would like to switch for another image,...
View ArticleError in conn_slice_display
Hi, first time conn user here. this is the Error I received when trying to load slice display for both anat and func .nii files. appreciate your help. ERROR DESCRIPTION: Unrecognized field name...
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