Changing default preview
Hello, is there anyway to change the default preview within the ICA Results to be of a saggital view rather than an axial view? From, Humza AHmed
View Articlecrash during the outlier detection
Dear Alfonso, I am encountering a repetitive error during the "functional outlier detection" step while I am trying to pre-process a 2 conditions drug vs placebo resting state dataset. I am thus...
View ArticleAnalysis step error, minimal denoising
Hello, I have preprocessed my data in SPM12 (slice-time correction, coregistration, segmentaion, normalization) and would like to perform ICA in CONN with minimal preprocessing and denoising. I have...
View ArticleRE: Preprocessing error, functional normalization
> Thanks for all your help! It turns out that there was nothing wrong with the raw volumes, and I did include all the default pipeline steps in the default order. The trick was to run the...
View ArticleDenoising Error, Updating Analysis variables
Hello, I receive this denoising error during step 6/6, updating analysis variables : ERROR DESCRIPTION: Index exceeds matrix dimensions. Error in conn_process (line 1712) else...
View ArticleRE: Feature request: relative path lookup
Thank you very much Alfonso for considering my feature request, and for the command I will certainly add to my conn subjects loader script! About why I need to re-compute, it's because of REX: if you...
View ArticleFeature request: 2nd level covar description
The second level covariates are used to construct the path where CONN stores the data for each experiment. The problem is that paths are limited to a certain length, and so if you have too many...
View Articletime series extraction
Hello Conn community, I have run a simple resting state analysis through first level seed to voxel. I want to extract the time series of my ROI after removal of white matter, motion, etc. In...
View ArticleROI-to-ROI Results explorer colorbar options
In the Results Explorer in ROI-to-ROI second-level results, how would one go about changing the default colorbar options - say I wanted to threshold all images from z -9 to 9?
View ArticleRE: Which timeseries to get right connectivity?
Hello Dr. Alfonso, when I load the ROI_Subject#_Condition#.mat document I see a data, d1data, and d2data. What is the differences between these?
View ArticleRE: Extracting PPI values
[color=#000000]Dear Erin,[/color] [color=#000000]For seed-to-voxel results the gPPI beta values are computed at each voxel (and they are stored in those BETA files). If you want to extract the average...
View ArticleRE: voxel-to-voxel cross-correlation
[color=#000000]Hi Joseph,[/color] [color=#000000]Please see this and related posts (http://www.nitrc.org/forum/message.php?msg_id=16378 )[/color] [color=#000000]Best[/color]...
View ArticleRE: Conn 16a Toolbox error during Analysis
[color=#000000]Hi Carlos,[/color] [color=#000000]The best solution is the first one (explicitly define the 'pre' and 'post' conditions in [i]Setup.Conditions[/i]). [/color]The second solution would...
View ArticleRE: Error in second level voxel2voxel stage
[color=#000000]Hi Pär[/color] [color=#000000]Sorry about that, could you please try the following and let me know whether that would fix this issue?[/color] [color=#000000]global CONN_x;[/color]...
View ArticleRE: Analysis step error, minimal denoising
[color=#000000]Hi Scott,[/color] [color=#000000]Could you please check in the first-level analysis definitions that you are entering in the 'sources' list only valid ROIs? (if you enter as sources, for...
View ArticleRE: crash during the outlier detection
[color=#000000]Dear Ali,[/color] [color=#000000]This is difficult to tell, hard crashes like this could indicate some issue with a corrupt datafile/filesystem, or they could indicate some issue with...
View ArticleRE: Changing default preview
[color=#000000]Hi Humza,[/color] [color=#000000]Sorry, not easily. Currently you could try something like the following:[/color] [color=#000000]a=spm_vol('conn/utils/surf/referenceT1.nii');...
View ArticleRE: REX Results GUI: Meaning of Effect Sizes
Dear Alfonso I have another question about the meaning of the [b]sign[/b] of the effect size in the REX displays: In the seed to voxel analysis "Treatment : Placebo : Score_Total_Treatment :...
View ArticleRE: Loading conn files in SPM
Hi all, I am not sure if anyone here will know the answer to this, but I figured I would give it a try. I am planning to use Dynamic Causal Modeling with SPM12 on some fMRI resting state data and was...
View ArticleAnticorrelations instead of correlations?
Hi, I'm running into a weird problem with a basic seed-to-voxel connectivity analysis. I'm using a seed in the PCC. For most of the runs and subjects I see the expected effect: the PCC seed activity...
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