[color=#000000]Hi Ami,[/color]
[color=#000000]My guess would be that this reflects a misalignment/miscoregistration between the ROI definition files and your functional data. Standard preprocessing steps in CONN are meant to bring all of your data to MNI space. If you are skipping this step simply make sure that all of your data is appropriately coregistered and in the same space as your ROI files. For example, you may:[/color]
[color=#000000] 1) in [i]Setup.ROIs[/i], select your ROI file (e.g. atlas) and click on '[i]ROI tools. Check ROI/functional coregistration[/i]'[/color]
[color=#000000] 2) in [i]Setup.functional click on 'functional tools. Check functional/anatomical coregistration'[/i][/color]
[color=#000000] 3) in the [i]Denoising [/i]tab, the display there is overlaying the structural data, functional data, as well as the analysis-mask used, so that is also a good place to detect if something looks incorrectly coregistered early on. [/color]
[color=#000000]Hope this helps[/color]
[color=#000000]Alfonso[/color]
[color=#000000]
[/color][i]Originally posted by Ami Tsuchida:[/i][quote]Hello,
I am running simple Seed-to-voxel/ROI-to-ROI functional connectivity (correlation) analyses from single-session resting-state data on 200+ subjects. I used already preprocessed and denoised functional data, and skipped all the preprocessing and demonising steps. Although with some trouble initially to set it up due to the large dataset, I was able to finish everything up to the second-level stage. However, when reviewing the first-level results, I noticed that they were not plausible. Just scanning the results of the first few subjects, some had negative values around the seed region and the homologous region in the opposite hemisphere, where one expects to find the strongest connectivity. I know that the first-level results can be noisy, but I expect to see positive values at least around the seed region.
I initially thought these were problems in data, but we processed the same raw data (preprocessed, denoised) using in-house program just to look at the seed-to-voxels connectivity, and I could see that in the same subjects, there are robust positive correlation around the seed region and homotopic area on the other hemisphere.
I looked inside various intermediate files, but could not find anything that's obviously wrong. I attached the example of BETA_Subject...nii (source is in Left Hippocampus), resultsROI...mat as well as ROI_Subject...Condition...mat from preprocessing for the same subject. I'm not sure whether these are enough to give you information about what went wrong, but please let me know if there is any other file I should attach.
Thank you!
Ami[/quote]
[color=#000000]My guess would be that this reflects a misalignment/miscoregistration between the ROI definition files and your functional data. Standard preprocessing steps in CONN are meant to bring all of your data to MNI space. If you are skipping this step simply make sure that all of your data is appropriately coregistered and in the same space as your ROI files. For example, you may:[/color]
[color=#000000] 1) in [i]Setup.ROIs[/i], select your ROI file (e.g. atlas) and click on '[i]ROI tools. Check ROI/functional coregistration[/i]'[/color]
[color=#000000] 2) in [i]Setup.functional click on 'functional tools. Check functional/anatomical coregistration'[/i][/color]
[color=#000000] 3) in the [i]Denoising [/i]tab, the display there is overlaying the structural data, functional data, as well as the analysis-mask used, so that is also a good place to detect if something looks incorrectly coregistered early on. [/color]
[color=#000000]Hope this helps[/color]
[color=#000000]Alfonso[/color]
[color=#000000]
[/color][i]Originally posted by Ami Tsuchida:[/i][quote]Hello,
I am running simple Seed-to-voxel/ROI-to-ROI functional connectivity (correlation) analyses from single-session resting-state data on 200+ subjects. I used already preprocessed and denoised functional data, and skipped all the preprocessing and demonising steps. Although with some trouble initially to set it up due to the large dataset, I was able to finish everything up to the second-level stage. However, when reviewing the first-level results, I noticed that they were not plausible. Just scanning the results of the first few subjects, some had negative values around the seed region and the homologous region in the opposite hemisphere, where one expects to find the strongest connectivity. I know that the first-level results can be noisy, but I expect to see positive values at least around the seed region.
I initially thought these were problems in data, but we processed the same raw data (preprocessed, denoised) using in-house program just to look at the seed-to-voxels connectivity, and I could see that in the same subjects, there are robust positive correlation around the seed region and homotopic area on the other hemisphere.
I looked inside various intermediate files, but could not find anything that's obviously wrong. I attached the example of BETA_Subject...nii (source is in Left Hippocampus), resultsROI...mat as well as ROI_Subject...Condition...mat from preprocessing for the same subject. I'm not sure whether these are enough to give you information about what went wrong, but please let me know if there is any other file I should attach.
Thank you!
Ami[/quote]