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help > RE: No BOLD variance in first level?
Mar 26, 2015 07:03 PM | Fred Uquillas
RE: No BOLD variance in first level?
Hi Alfonso,
If I may ask, I'm wondering what the opposite of this scenario would mean? As in, what if for CSF or white matter confounds one sees a heck of a lot of variance explained throughout the brain display?
All the best,
Fred
Originally posted by Alfonso Nieto-Castanon:
If I may ask, I'm wondering what the opposite of this scenario would mean? As in, what if for CSF or white matter confounds one sees a heck of a lot of variance explained throughout the brain display?
All the best,
Fred
Originally posted by Alfonso Nieto-Castanon:
Dear
Diana,
Your snapshot of the preprocessing step looks perfectly fine, the lack of suprathreshold voxels in the display only indicates that the contribution of your confounding effects is below 50% of the total variance in the BOLD signal (this is not uncommon; you may change the threshold value located below the display to see the voxels where the percentage variance explained is above the specified threshold). Regarding the first-level connectivity maps, if you could attach a similar display I might be able to tell you with more confidence, but this could also (potentially) be just a matter of the interpretation of the display figure (try increasing the threshold value, which represents there uncorrected voxel-level p-values, or shifting through the image using the slider located at the right of the display, to see if you can see suprathreshold voxels for your different subjects/seeds). Let me know if this helps clarify a bit.
Best
Alfonso
Originally posted by Diana Wotruba:
Your snapshot of the preprocessing step looks perfectly fine, the lack of suprathreshold voxels in the display only indicates that the contribution of your confounding effects is below 50% of the total variance in the BOLD signal (this is not uncommon; you may change the threshold value located below the display to see the voxels where the percentage variance explained is above the specified threshold). Regarding the first-level connectivity maps, if you could attach a similar display I might be able to tell you with more confidence, but this could also (potentially) be just a matter of the interpretation of the display figure (try increasing the threshold value, which represents there uncorrected voxel-level p-values, or shifting through the image using the slider located at the right of the display, to see if you can see suprathreshold voxels for your different subjects/seeds). Let me know if this helps clarify a bit.
Best
Alfonso
Originally posted by Diana Wotruba:
Dear Conn users
I am having some trouble with running the first level analysis in the newest version of Conn (13f).
I loaded the realigned, slicetimed and normalized functional images (analyze format) and the corresponding coregistered and normalized segmented images (wc1*, wc2*, wc*3). This went perfectly fine for some but not all subjects. In appr. half of the subjects there seems to be no BOLD variance explained for the confounds (which is improbable). Still the vx2vx connectivity distribution looks fine (the original distribution shifted to the right, centered without the confounds).
(Also in the first level analysis results, there are no connectivity maps displayed for the same subjects)
(motion derivative order 1, dimension 6; white matter /CSF derivative order 0 dimension 3).
Any help would be very much appreciated!
Best
Diana
I am having some trouble with running the first level analysis in the newest version of Conn (13f).
I loaded the realigned, slicetimed and normalized functional images (analyze format) and the corresponding coregistered and normalized segmented images (wc1*, wc2*, wc*3). This went perfectly fine for some but not all subjects. In appr. half of the subjects there seems to be no BOLD variance explained for the confounds (which is improbable). Still the vx2vx connectivity distribution looks fine (the original distribution shifted to the right, centered without the confounds).
(Also in the first level analysis results, there are no connectivity maps displayed for the same subjects)
(motion derivative order 1, dimension 6; white matter /CSF derivative order 0 dimension 3).
Any help would be very much appreciated!
Best
Diana
Threaded View
| Title | Author | Date |
|---|---|---|
| Diana Wotruba | Mar 15, 2012 | |
| Kristina Gelardi | Mar 21, 2016 | |
| Alfonso Nieto-Castanon | Mar 31, 2016 | |
| Kristina Gelardi | Apr 6, 2016 | |
| Alfonso Nieto-Castanon | Mar 20, 2012 | |
| Fred Uquillas | Mar 26, 2015 | |
| Alfonso Nieto-Castanon | Apr 6, 2015 | |
| Fred Uquillas | Apr 14, 2015 | |
| Diana Wotruba | Mar 24, 2012 | |