Invalid or incomplete JSON during preprocessing
Hello!

 I am new to CONN and I using the compiled version. I am trying to complete a preprocessing step using the preprocessing pipeline for volume-based analysis (direct normalization to MNI-space)...
View ArticleRE: CONN and fmriprep - error loading confounds
[color=#000000]Hi Ana,[/color] [color=#000000]Yes, you are right one alternative would be to manually edit those files and change the N/A values to 0. Another alternative would be to recreate those...
View ArticleRE: Pairwise time-series correlations in a mask
Hi Tamir, [color=#000000]Sorry that cannot be done simply from the GUI, but you could compute those average-correlation measures using something like:[/color] Maskfile = '/data/mymask.nii'; % ROI mask;...
View ArticleRegional Homogeneity (ReHo) in CONN
Hello Alfonso, Can ReHo be computed in CONN? Will computing LCORR with a kernel size equal to the voxel width be the same as regional homogeneity (ReHo)? Many thanks in advance, Mohammad
View ArticleRE: Problem with ALFF and fALFF analysis
Thank you Alfonso, The issue was fixed. I appreciate your help greatly. It was an issue with the Lab's drive and the subjects with missing ALFF values actually had missing BOLD data. Thanks again,...
View ArticleExtract BOLD timeseries physiological factor gPPI
Hi there, Would you be able to help with the following (and apologies if this has been asked before)? I have set-up a gPPI model with 5 conditions and I was wondering if it is possible to extract...
View ArticleRE: First-level analysis and exporting results
[i]Originally posted by Benson Stevens:[/i][quote]Hi Bryant, There is a brief description using the GUI in the CONN forum here: https://www.nitrc.org/forum/message.php?msg_id=13304 The raw files can be...
View ArticleSeed based Connectivity Analysis in CONN
Hello Everyone, I am performing a SBC analysis on resting state data on 3 groups of subjects. After preprocessing my data into conn, I tried to export my roi in the ROI option in the SETUP tab and...
View ArticleRE: Selecting Voxel Mask
Hi, I have the same question. Just bumping it if someone can verify. From what I understand, specifying implicit mask means that voxel-voxel analysis will be in the subject space and not in MNI space....
View ArticleRE: Studying rs- fMRI in individual subjects is the new mainstream?
Dear Kasia, Thank you for sharing your experience. I would say that all types of analysis are mostly done to make a prediction about a group because we usually want to generalize the results to a...
View ArticleRE: use default Tissue Probability Map option
Dear Marianna, Tissue probability maps are included at the segmentation step. So if you choose one of the default preprocessing pipelines that contain segmentation, a GUI will pop up when you will...
View ArticleExport mask
Hi Alfonso and all CONN experts, In the Results Explorer window under the clusters list there is a list of the corresponding areas from the Harvard-Oxford atlas for each identified cluster in the...
View ArticleProblem while I work with anothers data
Hello I have this problem while I work with anothers data ERROR DESCRIPTION: Error using conn_menu>conn_spm_read_vols (line 1091) Error reading file /Applications/conn/utils/surf/referenceT1.nii....
View ArticleGood atlas for ROI-to-ROI analysis
Dear all, As things evolve with time, I wanted to ask for current suggestions for a well-established brain atlas for ROI-to-ROI analysis. Thank you, Lucas
View ArticleQC variables are not moved to 2nd level analysis tab
Hi everyone, I have recently switched to conn 19c. It is awesome as usual, except for the fact that QC variable calculated during preprocessing and denoising are not automatically moved to 2nd level...
View ArticleImport conditions informations from a text file, in an event-related desing +...
Dear Dr Alfonso Nieto-Castanon, I would like to carry out a gPPI analysis with the CONN toolbox. I am facing several issues: [u]1. Import conditions informations from a text file[/u] To set...
View ArticleRE: ROI-to-ROI menu error.
[color=#000000]Dear Romke,[/color] [color=#000000]That is curious, it seems there is a mismatch between the number of subjects in your study and the number of subjects' data stored in your ROI-to-ROI...
View ArticleRE: Regional Homogeneity (ReHo) in CONN
[color=#000000]Hi Mohammad,[/color] [color=#000000]Yes, LCOR, computed as the average connectivity between a voxel and its neighbors, is a measure of regional homogeneity, as it measures the similarity...
View ArticlePermutation testing in ROI-ROI analyses
Hi, In past versions of Conn (~17f), I was able to threshold and enable permutation testing in the ROI-ROI second level analysis results explorer. In the newest version of conn (19c), the results...
View Articleadjusted betas after 2nd-level analysis
Dear Alfonso, thank you for the great toolbox! How can I extract adjusted/corrected betas of my the 2nd-level analysis? As I have understood from this post...
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