How is functional data matched to MNI grey matter template without a fieldmap?
Apologies if this has been addressed in this forum before. I couldn't find any relevant posts. I'm aware that CONN uses several SPM functions, including DARTEL and the Unwarp Toolbox, to do its work....
View ArticleIntensity Normalization: Where and When?
Dear all, After analyzing and visualizing the functional preprocessed data (montage; attached) of my subjects, I realized most subjects show dark-inside fMRI scans (hollow-resembling) while others do...
View ArticleRE: Dark Lines in the connectivity matrix
Dear Alfonso, Thank you so much for your comments! Yes, for problematic participants, there is no enough coverage in the functional data due to the sequence distortion. Best, Gucy
View ArticleRE: error message: ROI-to-ROI first level
Dear Alfonso, I am posting again to get a reply from you. Please share the contact info with me in order to send my conn_*.mat file. Thank you!
View ArticleIs hemodynamic lag / delay accounted for
<script id="th-iframe-script" src="chrome-extension://ofdopmlmgifpfkijadehmhjccbefaeec/assets/comms/commsiframe.js"></script>Hello all, Have been reading around but still unsure. I am...
View ArticleRE: Error extracting Grey Matter BOLD signal for subject 1 session 1
SOLVED! Duplicate versions of rex, needed to remove other call to rex from filepaths. Thanks!
View ArticleError with ART functional outlier detection
I am completing preprocessing using the default surface based stream beginning a gPPI and I am getting this error. Any advice would be helpful. ERROR DESCRIPTION: SWITCH expression must be a scalar or...
View ArticleHow to find slice order?
Hello! Just starting out learning how to use the CONN toolbox and I'm practicing with a single subject's data. I'm at the point where I need to select the slice order but I'm actually not sure how to...
View ArticleExport Mask with only 1 Cluster after GCOR
Hello My results for GCOR produce different clusters, but when I highlight the cluster and then select export mask, it creates a mask that includes all clusters. I simply want to create separate masks...
View ArticleMotion
Dear Conn experts, i am somewhat new to Conn and fmri analyses. I am currently working with a rsfmri dataset of a population with cervical dystonia (vs controls). In this sample there is a substantial...
View Articlesimult vs RegBP at the denoising step
Hi. The distributions before and after denoising looked pretty much bell-shaped, when the Band-pass filter option was set to 'RegBP.' But, when I set the Band-pass filter option to 'simult,'...
View ArticleRepetition Time for resting state analysis-- CONN
Hello again all! I'm about to start using CONN's basic pre-processing pipeline for my resting state data. In 'Setup', I am now entering the number of subjects that I have, number of sessions,...
View ArticleMerging projects using Conn 20b
Hello, I have a large dataset I am working with (~1000), and have previously posted about some difficulties I've had with scheduling it to run parallel on our HPC. I have gotten it to work with...
View ArticleWrong dimensions error during denoising
Hi there, I imported 1 participant into CONN using fmriprep data (preprocessed anatomical and functionals in MNI space). For the preprocessing pipeline I only selected the options to create a vdm,...
View Articlevoxelwise analysis for secondary dataset
We would like to run conn analyses on both volumes and surfaces for the same dataset. Is it possible to include the volumes as a secondary dataset, but still have the volumes go through denoising and...
View ArticleRE: multisite data harmonization using CONN outputs?
[color=#000000]Hi all,[/color] [color=#000000]I have a similar question, but can't find an answer on the forum.[/color] [color=#000000]What files would you recommend sending for harmonization? [/color]...
View ArticleRE: matrix of TFCE values from ROI-to-ROI analysis
[color=#000000]Dear Raul,[/color] [color=#000000]The 'Export Mask' button in the R2R results explorer window will save a file with the TFCE scores for each individual connection[/color]...
View ArticleRE: Intensity Normalization: Where and When?
[color=#000000]Dear Amir,[/color] [color=#000000]That's an interesting question. There is no voxel-specific intensity normalization step that is typically applied to the functional data. There is a...
View ArticleRE: Export Mask with only 1 Cluster after GCOR
[color=#000000]Hi Raul,[/color] [color=#000000]When using the 'export mask' button, if your target file is named myfile.nii, then, in addition to the file [b]myfile.nii[/b] with the stats for all...
View ArticleRE: simult vs RegBP at the denoising step
[color=#000000]Hi Chloe,[/color] [color=#000000]The QC distribution will become flat, and in extreme cases just bimodal over the extreme 0/1 values only, when the effective degrees of freedom of the...
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