RE: The description of V1 V2 V5 ROIs in CONN toolbox
[i]Originally posted by Zengjian Wang:[/i][quote]Anyone knows the defination of V1 V2 and V5 rois in CONN toolbox please? How to get thses ROIs?[/quote] [color=#000000]Are V1/V2/V5 available as seeds...
View ArticleRE: Reducing Disk Storage Use
Dear Alfonso, Thank you very much for the clarification. That is exactly what I was looking for. I must have checked this option by mistake and did not realize it. Kind regards, Amr
View ArticleRE: Covariate of interest
Hi Alphonso, I had not go back on this project until now. I saw your answer so : thank you very much! Also, you said I was correct about the design. However, now somebody told me that if I want the...
View ArticleError in set up
Dear CONN experts, Following the tutorials, I used the Import option to select 1st level 'SPM.mat' files. It automatically selected all preprocessed functional images, conditions and 1st level...
View Articlenormalization of caovariate?
hi, in the covariates ; do I have to enter normalized value ? for example for the age, i must insert the age of each individual subject or I have to normalize the value and insert this? other question...
View ArticleniftiDATA output files stacked?
Dear all, I'm interested in the preprocessed denoised data (in nii files). I already know these are to be found in the results/preprocessing folder in the format of...
View Article2nd Level effects of diagnosis
Apologies if this has been answered extensively, and feel free to link me if it has, but I searched through the forums as best I could before posting. Question 1.) In the second-level covariates within...
View ArticleRE: Motion measure AFTER scrubbing
[color=#000000]Dear CONN Users,[/color] Is it possible to look at the motion measures separately for pre-post for valid scans only? I understand that to do so a new condition should be created, but...
View ArticleMissing Covariates (use of NaNs), and what scan data should be included
Hello All I am running a linear regression model where I have some missing covariates that are continuous (CSF_biomarker data). For those that are missing I have labeled them as NaNs (eg: 3 1 5 NaN 6...
View ArticleCompCor questions
Hi Alfonso, I read many of your posts in which you mention that CONN uses CompCor for the denoising step. I was wondering what exactly is CompCor doing, does it simply regress out the WM and CSF, or...
View Articleafter denoising, the Beta images have different number of slices
Dear expert, Recently, I am using Conn to analysis my resting state fMRI data. However, I found that after the denoising step, the slices number in different beta images are not the same. So I want to...
View ArticleHow to transform a subset of MNI-space first-level maps to native space for...
Dear CONN experts, I have preprocessed all my subjects in CONN v18 in MNI space. Now, I would like to convert the resulting MNI-space seed-to-voxel and ICA maps for each subject to native space, in...
View ArticleRE: conn gui error in 2nd level results display
Hi All, I am using CONN (version 18a) on SPM12 with a resting-state ADNI dataset. When I performed seed-voxel analyses, it worked perfectly fine at second-level but when I repeated the analyses to...
View ArticleRE: second-level analysis in Conn
Hello, I was wondering if someone can help me understand how to interpret results when running the test to look for difference between group1 and group2 in their association between symptom scores and...
View ArticleQA normalization plots
Hi, I'm having a strange problem with the QA normalization plots. On a few of the slices, the MNI TPM template outline only covers a small part of the area. I've attached a screenshot. It happens for...
View ArticleRE: Preprocessing error, functional normalization
[i]Originally posted by Neir Eshel:[/i][quote]> 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...
View Articlebasic question about gPPI conditions
Hi Alfonso and conn experts, I am trying to do a gPPI analysis on a task with the following components: 1) instruction period 2) task condition A 3) task condition B 4) task condition C 5) affect...
View ArticleWeighted ROI using seed map
Dear Alfonso, dear CONN community, for a seed-to-voxel analysis based on Fox et al. (NeuroImage, 2013), I would like to use a second-level connectivity map from a previous analysis as a weighted ROI....
View Articlere-run denoising and first-level for individual subjects
Dear experts, After running the first-level analysis I realized that a few subjects were incorrectly preprocessed. I already preprocessed them individually, but I was wondering if there is a way to...
View ArticleRE: preprocessing physiological data
Hello Alfonso, Is it okay to add the RETROICOR regressors after the preprocessing pipeline? or they have to be regressed before some preprocessing steps like slice time correction and spatial...
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