Reoriented, not realigned, all data in SPM12
Dear Expert, I set origin and reoriented the structural and functional MRI manually in SPM12. The orientation parameters were saved as .mat files. I did not do realignment. I imported reoriented...
View ArticleBOLD MB Acquisition (and preprocessing issue)
Good morning I did a test run through the standard CONN pipeline for a single subject for 8 runs of task free BOLD data. When I got to the second step where it was necessary to specify conditions, it...
View Articlevdm file generation
Dear Alfonso, I added a new secondary fmap dataset (double-echo sequence). I don't understand the next step, how to run using the gui 'functional_vdm_create' (and how I can add in the setup "read...
View ArticleRE: ART regression timeseries output
[color=#000000]Hi Airi,[/color] [color=#000000]The "art_regression_timeseries*.mat" files contain the [b]two[/b] raw timeseries which are used internally by ART for determining outliers -simply by...
View ArticleRE: Convert Matc to nii
[color=#000000]Hi Hongru,[/color] [color=#000000]You may be misremembering and the command [b]conn_matc2nii [/b]is probably the one you intended to run? That converts CONN"s internal .matc files to...
View Articlescrubbing-explanation
Hi Alfonso, I have selected the default pipeline to preprocess my scans in CONN. My question concerns the ART toolbox. Does the threshold selected (either conservative, intermediate or liberal) apply...
View ArticleExtract ROI BOLD time series from different conditions
Hi: I am doing a longitudinal study with two set of data at two different time points, indicated by visit 1 and visit 2. When I was trying to extract the ROI BOLD time series from result/preprocessing,...
View ArticleWhy the mean of the correlation distribution should be zero after denoising?
[b]Dear Conn experts,[/b] I can understand why the correlation of voxels (functional connectivity of voxels) should have a normal distribution but I don't know why the mean of this distribution should...
View ArticleRE: Brain modularity
[color=#000000]Hi Tamir,[/color] [color=#000000]No, sorry, see BCT (https://www.nitrc.org/projects/bct) for several modularity measures (and many other interesting graph measures)[/color]...
View ArticleRE: fMRIPrep import
[color=#000000]Hi Adam,[/color] [color=#000000]Regarding (1) yes, that is the default behavior. If computing run- or condition- specific measures is more appropriate for your study, you may do so from...
View ArticleRE: Is it possible to integrate CONN with Python?
[color=#000000]Hi Akhila,[/color] [color=#000000]I have not tried this myself, but there are a number of different ways to integrate Matlab and python pipelines. You may want to see...
View ArticleRE: covariate scrubbing mismatched dimensions
Dear Alfonso, I realised that the mistake is because of removing initial scan after all preprocessing completed. Now I did again which shows same dimension. Thank you very much for your suggestion. I...
View ArticleSelecting QC co-variate
Dear Alfonso, I did preprocessing steps as mentioned in the conn manual for fMRI analysis. After preprocessing, there are 7 co-variate included automatically as shown below. 1. All subjects 2. QC Valid...
View ArticleRE: Denoised result in different space dimensions
Dear Alfonso, setting batch.Setup.voxelresolution = 3; so to functional dimensions works fine in respect to voxelsize and x-,y-,z-dimensions. However, my problem with the huge file size is not solved...
View ArticleDenoised nifti DATA as input to GIFT toolbox
Dear Conn-experts, I´m planning to use the denoised nifti output from CONN as input to the GIFT toolbox. I used the function conn_matc2nii.m to convert the matc files in the results/preprocessing...
View ArticleContrasts for repeated measures design
Dear experts, I would like to study the change in connectivity across sessions between groups. I have defined the contrast as follows: GroupA GroupB [1 -1] Baseline-session_1 Task-session_1...
View ArticleSkipping segmentation
Hello All, I have binary segmentations of grey matter, white matter, and other rois made outside of CONN that I am trying to import. I am able to successfully define these via a batch script. I am not...
View ArticleRE: Extract ROI BOLD time series from different conditions
[color=#000000]Hi Renxi,[/color] [color=#000000] Need more details, but possibly the following post may address what you are referring to? https://www.nitrc.org/forum/message.php?msg_id=13863[/color]...
View ArticleInterpretation of gPPI results
Hi, I have data from an event related study in which participants had to respond to either a green or red stimuli (i.e., two conditions: Red vs Green). Additionally the participants were either...
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