Combining FSL partially preprocessed data (MCFLIRT; Topup) with CONN
Dear all, I have partially fMRI data preprocessed in FSL, that I put into Conn to finish preprocessing and subsequently run an FC analysis. Looking at the 1st level covariates after preprocessing, I...
View ArticleRE: importing existing connectivity matrices in CONN
Dear Alfonso, The conn-module command we used is the following: conn_module( 'glm' , ... 'data', 'med100sujetsp.mtx.nii', ... 'design_matrix', X, ... 'contrast_between', C, ... 'folder',...
View ArticleSecond-level analyses setup for behavioral measure regression for a single group
Hi Alfonso and CONN forum members: I am having some conceptual issues with setting up my second-level analyses, and I'm hoping to receive your advice as to what the best setup would be. If you don't...
View ArticleRE: Error Set up functional data
Dear Alfonso, After trying the conn_getinfo.m patch you sent me by email (18-11-2020), there is still an error. ERROR DESCRIPTION: ERROR: Subject 1 Session 2 first-level covariate realignment...
View ArticleDenoising CSF confound
Hello, I have a problem with the denoising of my resting state images. So i have [b]one subject[/b] that i want to compare to [b]36 other healthy subjects[/b]. I have [b]2 groups of healthy...
View ArticleQuestion about output file and units
Hello, I'm trying to find the output file which contains the time series for each voxel, after denoising. In the 1st level analysis in the GUI, I have the option of clicking on a given voxel for a...
View ArticleNo option to select gPPI as analysis type from Analyses (1st level) tab
Hi All, Quick question. It's my first time running analyses using CONN and I'm attempting to run gPPI. I've gotten through everything up to the first-level analyses, but now when I try to select my...
View ArticleRE: reference to non-existent field 'filename'
[i]Originally posted by Romke Hannema:[/i][quote]Dear Alfonso, Thank you for your response. I may have phrased my original question poorly. I am not writing a batch script, but just using the GUI and...
View ArticleChanges to Structural Segmentation/Normalization?
Have there been recent changes to how CONN handles structural segmentation and normalization? I've noticed, using the same dataset, that segmentation and normalization came out better in earlier CONN...
View ArticleDenoising for task related fMRI and using different toolboxes
Dear Conn Community, I have a specific issue and would appreciate<span style="white-space: pre;"> </span>your input and your experience on this topic. I was recently introduced to the Conn...
View Articledefining the post-hoc test contrats
Dear All, I have a question regarding the post-hoc tests / contrasts in CONN toolbox. I have 3 groups (AD, MCI, HC respectively) and I conducted first F tests using the [-1 1 0;0 -1 1] contrast. I...
View ArticleNetworks.nii: only one ROI displayed
Dear Alfonso, First of all, thank you so much for this toolbox which is absolutely great! Just a quick question. I'm trying to extract the masks of some of the predefined network ROIs. I opened...
View ArticleChanging Analysis Mask
Dear Alfonso and all, My team and I are all currently trying to work on the same project in CONN, and we are looking for solutions to a mask issue. I am planning to run a ICC on a subset of the...
View ArticleRE: Beta values
[color=#000000]Hi Mickael,[/color] [color=#000000]The beta value for a two-sample t-test is the difference between the average Fisher-transformed correlations between the two groups[/color]...
View ArticleRE: Contrast specification for Group comparison in a multi-center RCT...
[color=#000000]Hi Till and Marcel,[/color] [color=#000000]Regarding over-parametrized models, that is perfectly fine. The general linear model handles rank-deficient design matrices without any...
View ArticleRE: HPC - SLURM - Parralellisation with conn
[color=#000000]Dear Sophie,[/color] Let's try to solve one thing at a time. First, the BATCH_12012021.mat contains the details of the batch structure that (I imagine) your Lesion*.m script is creating,...
View ArticleRE: Question about output file and units
[color=#000000]Hi David,[/color] [color=#000000]The denoised timeseries are only saved into a CONN's internal .matc format (which makes reading data from individual slices faster to make the GUI more...
View Articledifferent results in preview and results explorer
Dear all, I am currently using CONN v 19.c and working on second-level ROI-to-ROI analysis between patients and controls. I put a [1, -1] design matrix to see the difference between the groups, and 1...
View ArticleRE: Slice Timing correction with multi-site data
Hey all together, I now this one is old. Still I will try to catch up with this. In my point of view somebody (like me) would need a covariate for EVERY site like: site 1 [1 1 1 0 0 0] site 2[0 0 0 1...
View ArticleRE: Minimum T-values in ROI-to-ROI
[i]Originally posted by Andreas Voldstad:[/i][quote]Dear CONN experts, I am exporting the results of positive and negative T-tests from the ROI-to-ROI results explorer, involving multiple ROIs, in...
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