using a mask in conn/utils/otherrois/buildP.m
Dear Alfonso, I am trying to use the buildP.m provided in CONN/utils/otherrois. My idea is to generate 1.5mm cubes only within a mask (e.g. within DMN or other networks) instead of the whole brain. I...
View ArticleRE: Single subject analysis
Dear Steven, According to what Alfonso wrote, :"The files named "BETA_Subject#_Condition#_Source#.nii" (...) contain the Fisher-transformed correlation values between each seed/source and the rest of...
View ArticleRE: REX Results GUI: Meaning of Effect Sizes
Dear Alfonso I have a follow up question, but first I want to thank you again for your previous help. We ran the analyses as you recommended. Now a reviewer pointed out that our analysis as above...
View ArticleCompatibility CONN toolbox with Matlab R2017b
Dear community, as I my mac was recently uploaded to High Sierra (version 10.13.2) I will soon have to use Matlab R2017b which apparently works most reliably with this macOS version. Does anybody of...
View Articlemissing BATCH.Setup.preprocessing.sliceorder in...
Hello, Concerning the sample script "conn_batch_humanconnectomeproject.m", is it missing the line that defines slice order? Based on the Human Connectome Project Sessions Protocol...
View ArticleOutputs change folders
Regarding outputs, is there a way to send the output images (realigned, normalised, etc..) directly to a different folder from the original ones? This is because I want to preprocess the same subjects...
View ArticleConnectivity matrix for task data
Dear CONN experts, I have a question regarding the calculation of connecitivity matrices in CONN. I am analysing task data with two conditions: during one scanning session, participants experience...
View ArticleInformation on ROIs provided by CONN
Hi, I have some questions about the atlas and networks ROIs provided by CONN: Is it possible to confirm that when using these ROIs: -Networks ROIS: the average signal from a 10 mm sphere around the...
View ArticleImpact of sphere size (4 vs. 6 or 8 or 10 mm)
Hi CONN users, can anyone help me figuring out the impact of sphere size on the results? What are the advantages/disadvantages of using smaller vs. larger spheres? Anything would help (experiences,...
View ArticlePreprocessed and denoised data
Dear Alfonso Dear All I wonder where I can find in Conn the preprocessed, denoised, band-filtered and possibly z-scored subject/session data? And in which format? For further use in other software. I...
View ArticleRE: Changing the atlas and MNI positions
[color=#000000]Dear All[/color] Where can I find the MNI coordinates correspond to the predefined regions listed in the atlas.txt? Thanks for considering my request. Best wishes Larry [i]Originally...
View ArticleREX
Hello Dears, I have used REX to generate the connectivity values for each ROI and the output files for each ROI is a set of numbers (as stated below). I was wondering if someone could tell me what each...
View ArticleSlice timing 'Manually define'
Dear CONN-experts During slice time correction, let's say that my slice order is in a default setting on Philips Intera 3T scanner (48 slices), so 1,3,5,7,...2,4,6,8 etc. When using the GUI, in the...
View ArticleCluster extent thresholding of first-level connectivity maps
Dear CONN community, In my single case study I would like to report first level maps of my patient. I have already figured out (with a big help from this forum, for which I am very grateful!) how to...
View Articleerror in pre-processing step after flipping left/right hemispheres
Hello everyone, I am facing the following error in the pre-processing step in CONN version 17.f. I would appreciate if you let me know why is that and how I can fix it. a background about what I have...
View ArticleCONN's non-parametric and TFCE toolbox
[color=#000000]Dear CONN-experts[/color] This is what I have done so far. [list=1][*]Original F-test: eye(5)-1/n for Group1, Group2, Group3, Group4, Group5 (Looking for effects of interest)[*]Between...
View ArticleHelp with
Hi all, I have been using to make comparisons between two groups of patients based on cognition state. In the second level analysis, I make a [1 -1] contrasts and then check the differences using both...
View ArticleHow to use mask on CONN
Hi, I work with stroke patients and I dont know in which step should I insert the lesion masks on conn. Someone could help with this information? - How can I work with lesion masks on conn and how...
View ArticleCONN analysis: group comparision after intervention
Dear experts, The analysis I am trying to perform should show whether a certain intervention shows an effect. We have 2 groups who we want to assume are equal at time point 1. Each group is assigned to...
View ArticleRunning mediation with CONN
Hi Alfonso, I have done all the preprocessing and ROi-to-ROI and seed-based analyses of my data. Now I would like to investigate whether the functional connectivity between two regions is mediated by...
View Article