[Freesurfer] Seed-based fcMRI: mean BOLD post nuisance regressor

[Vinke, Louis N.,PHD]

Hello,
After running a seed-based connectivity 1st level analysis on an individual 
subject, is it possible to pull out the mean BOLD activation (across all 
time-points; all runs) in a way that any “noise” in the time-series has already 
been regressed out (i.e., motion, ventricle, csf, wm, global mean, high/low 
pass filter)?  I imagine it is one of the outputs in the analysis folder and 
not found within any particular FC seed sub-folder (containing pcc.nii.gz, 
etc.).  In other words, one may run different seed-based connectivity analyses, 
but the mean activation estimate will not change so long as the nuisance 
parameters stay the same.

The meanfunc overlay looks to be what I’m interested in, but unclear if this is 
created after regressing out nuisance parameters.

Thanks.
-Louis
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Re: [Freesurfer] Seed-based fcMRI: mean BOLD post nuisance regressor

[Douglas N. Greve]

Hi Louis, yes, meanfunc is after all regresssions, etc.
doug


On 3/28/2023 12:08 PM, Vinke, Louis N.,PHD wrote:


Hello,

After running a seed-based connectivity 1^st level analysis on an 
individual subject, is it possible to pull out the mean BOLD 
activation (across all time-points; all runs) in a way that any 
“noise” in the time-series has already been regressed out (i.e., 
motion, ventricle, csf, wm, global mean, high/low pass filter)?  I 
imagine it is one of the outputs in the analysis folder and not found 
within any particular FC seed sub-folder (containing pcc.nii.gz, 
etc.). In other words, one may run different seed-based connectivity 
analyses, but the mean activation estimate will not change so long as 
the nuisance parameters stay the same.


The meanfunc overlay looks to be what I’m interested in, but unclear 
if this is created after regressing out nuisance parameters.


Thanks.

-Louis


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The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
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Please note that this e-mail is not secure (encrypted).  If you do not wish to 
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