RE: How does the CONN calc compute GLM stats?
Thank you so much Alfonso for the clear and detailed explanation. I've been spending a lot of time diving into the code and details behind CONN and as a consequence, have been growing increasingly...
View ArticleICA: Parameter Choice and 2nd Level Effects ?
Dear fellow CONN-artists, I've recently begun diving in ICA based methods for extracting functional networks in a modestly large data set (110 subjects, 3 time points). One major question when running...
View ArticleError in second level voxel2voxel stage
Hi CONN experts, Need help with the following error at second level voxel2voxel stage. ERROR DESCRIPTION: Reference to non-existent field 'Y'. Error in conn (line 5078)...
View Articleno swar files
Hi, I followed the first default preprocessing pipeline (including functional to structural registration, as suggested by Alfonso:http://www.nitrc.org/forum/forum.php?thread_id=7155&forum_id=1144)....
View ArticleRE: ICA - extracting time series from components
I *think* the time series might be saved for each subject in the results/firstlevel/voxel2voxel subfolder in the ICA.Timeseries.mat file. You can try loading it in MATLAB and seeing if they contain...
View ArticleCONN Standalone Job Submission
I am trying to use the conn15g standalone version to submit a job from the GRID menu. I have not had problems using the GRID settings on the regular conn toolbox. Here is the output of the terminal...
View ArticleRE: Graph theory after 1st level regression
[color=#000000]Hi Alfonoso,[/color] [color=#000000]I would be very grateful if you answer my query.[/color] [color=#000000]Thanks[/color] [color=#000000]Shukti [/color][i]Originally posted by Shukti...
View Article"effect of rest": what can results mean?
Dear conn users, Playing with my data, I realized an "effect of rest" was added in recent versions of conn. I looked at the effects I had in a ROI to voxel analysis of fMRI data and was very surprised...
View ArticleRE: Result Explorer
Hi Alfonso, Thank you very much for your response. We ran the analysis and the results look great. I am trying to understand the data displayed under the statistics table. I have attached a screen shot...
View Articlephase shift of low-frequency periodic signal
Dear all, I used CONN to analyze a set of resting-state and task-induced data in two groups of participants, and found significant negative correlation in both groups. Some of negative correlation...
View ArticleRE: confound corrected nifti header shows TR 1
Hi Rajeev, I am having the same problem with some old data that has been already processed. Have you managed to find a solution to correct this? Thanks so much! Cheers, Patricia
View ArticleGlobal signal calculation
Dear Dr. Alfonso/Conn Users, Greetings! Thank you for the many detailed discussions on global signal on other threads. Based on that, I wanted to confirm the method by which Conn calculates the global...
View Articlepreprocessing prefixes
Can someone point to a list of prefix definitions for the preprocessing through Conn? I have run the default preprocessing pipeline for volume based analysis (direct normalization) and wondering what...
View ArticleRE: registration problem
[color=#000000]Hi Heidi,[/color] [color=#000000]'r' in SPM file naming convention is usually added to file names as prefix when reslicing is performed. Given Dr. Alfonso's suggestion, I think you might...
View ArticleRE: ART output
Hello Alfonso, Can framewise displacement and ART's composite motion measure be compared to each other ? In other words, can average FD and average composite motion (using the CONN option:...
View ArticleDenoised Data files
Dear all, According to what I've read in this forum (e.g. here http://www.nitrc.org/forum/message.php?msg_id=11244), CONN should create nifti-files of the denoised data. However, in the folder...
View ArticleTwo different contrasts on the same surface
Hi everyone, I wonder if there is a way of overlaying the results of two different contrasts (e.g. correlation between seed A connectivity with age, correlation between seed B connectivity and age)...
View ArticleExplanation of Outputs
<span style="white-space: pre;"> </span>Hello Alfonso and CONN users, I am looking for an explanation of the outputs of CONN (ie. data and results folders and their various outputs) I want...
View Articleflexible ANOVA spreading interaction
Dear All: In our study, we'd like to test the treatment effects in patient group, as compared with control group. Our hypothesis is the treatment will normalize Amygdala-prefrontal connectivity (more...
View ArticleSiemens Prescan Normalization
We have acquired resting state data on Siemens Skyra. Unfortunately, Prescan Normalization was turned off. This has resulted in moderate image intensity shading from the center out (dark in the center...
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