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help > RE: Multi-session pre-post design QC_ValidScans for each separate session
Jan 17, 2019 08:01 PM | Alfonso Nieto-Castanon - Boston University
RE: Multi-session pre-post design QC_ValidScans for each separate session
Hi Daniel,
To compute condition-specific QC_InvalidScans measures you may:
1) go to the Setup.CovariatesFirstLevel tab, select the covariate named 'scrubbing' and click on the 'covariate tools. compute new/derived 2nd-level covariates' option (in older CONN versions this was named 'covariate tools. compute summary measures' if I recall correctly)
2) in the new gui, select the following options: (with the changes it should look like the attached example image)
consider covariate scrubbing: raw values
summarize across timepoints: sum
summarize across dimensions: sum
summarize across dimensions first: checked
condition-specific measures: checked
That will create two new second-level covariates, each summing the number of invalid/outlier scans for one condition (i.e. like QC_InvalidScans but separately for each condition).
If you prefer instead to compute QC_ValidScans directly you may do so by using in step 2 above the following options instead:
consider covariate scrubbing: raw values
summarize across timepoints: user-defined (and when prompted enter "sum(1-x,1)" -without quotes- as your user-defined function)
summarize across dimensions: sum
summarize across dimensions first: checked
condition-specific measures: checked
and that will create two new second-level covariates, each summing the number of valid/non-outlier scans for one condition (i.e. like QC_ValidScans but separately for each condition).
Hope this helps
Alfonso
Originally posted by Daniel Westfall:
To compute condition-specific QC_InvalidScans measures you may:
1) go to the Setup.CovariatesFirstLevel tab, select the covariate named 'scrubbing' and click on the 'covariate tools. compute new/derived 2nd-level covariates' option (in older CONN versions this was named 'covariate tools. compute summary measures' if I recall correctly)
2) in the new gui, select the following options: (with the changes it should look like the attached example image)
consider covariate scrubbing: raw values
summarize across timepoints: sum
summarize across dimensions: sum
summarize across dimensions first: checked
condition-specific measures: checked
That will create two new second-level covariates, each summing the number of invalid/outlier scans for one condition (i.e. like QC_InvalidScans but separately for each condition).
If you prefer instead to compute QC_ValidScans directly you may do so by using in step 2 above the following options instead:
consider covariate scrubbing: raw values
summarize across timepoints: user-defined (and when prompted enter "sum(1-x,1)" -without quotes- as your user-defined function)
summarize across dimensions: sum
summarize across dimensions first: checked
condition-specific measures: checked
and that will create two new second-level covariates, each summing the number of valid/non-outlier scans for one condition (i.e. like QC_ValidScans but separately for each condition).
Hope this helps
Alfonso
Originally posted by Daniel Westfall:
Good afternoon
I have a pre-post design with resting state scans. For both the pre and the post I have two sessions of resting state scan. My setup in conn has 183 subjects each with 4 sessions (2 pre and 2 post scans). Then within the condition setup I differentiate between the scans for pre and the scans for post. When I run the ART and look at the 2nd level covariate QC_ValidScans I am finding that this is the total # of ValidScans collapsed across all 4 sessions. However, I am interested in making sure there is enough usable scan data (at least 5 minutes) for pre and for post separately.
Is there any way to separate the QC_ValidScans for pre and QC_ValidScans for post as defined by the condition setup, or, if not, is there is a way to just split it by session and I can calculate the total number of ValidScans from there?
Thank you!
Daniel
I have a pre-post design with resting state scans. For both the pre and the post I have two sessions of resting state scan. My setup in conn has 183 subjects each with 4 sessions (2 pre and 2 post scans). Then within the condition setup I differentiate between the scans for pre and the scans for post. When I run the ART and look at the 2nd level covariate QC_ValidScans I am finding that this is the total # of ValidScans collapsed across all 4 sessions. However, I am interested in making sure there is enough usable scan data (at least 5 minutes) for pre and for post separately.
Is there any way to separate the QC_ValidScans for pre and QC_ValidScans for post as defined by the condition setup, or, if not, is there is a way to just split it by session and I can calculate the total number of ValidScans from there?
Thank you!
Daniel
Threaded View
| Title | Author | Date |
|---|---|---|
| Daniel Westfall | Jan 17, 2019 | |
| Alfonso Nieto-Castanon | Jan 17, 2019 | |
| Jose Maximo | Mar 6, 2019 | |
| Alfonso Nieto-Castanon | Mar 7, 2019 | |
| Daniel Westfall | Jan 25, 2019 | |
| Daniel Westfall | Jan 25, 2019 | |
| Alfonso Nieto-Castanon | Jan 25, 2019 | |
| Daniel Westfall | Jan 25, 2019 | |