help > Multi-session pre-post design QC_ValidScans for each separate session
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Jan 17, 2019 06:01 PM | Daniel Westfall
Multi-session pre-post design QC_ValidScans for each separate session
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
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
Jan 25, 2019 02:01 PM | Daniel Westfall
RE: Multi-session pre-post design QC_ValidScans for each separate session
Sorry for the slow followup. Worked out great, thank you!
Jan 25, 2019 04:01 PM | Daniel Westfall
RE: Multi-session pre-post design QC_ValidScans for each separate session
As a quick followup, is there a similar way to do the same thing
but for the motion and GS parameters (Max and Mean)?
Thank you again
Thank you again
Jan 25, 2019 06:01 PM | Alfonso Nieto-Castanon - Boston University
RE: Multi-session pre-post design QC_ValidScans for each separate session
Hi Daniel,
Yes, to compute condition-specific QC_MeanGSchange and QC_MeanMotion measures you may:
1) go to the Setup.CovariatesFirstLevel tab, select the covariate named 'QC_timeseries' and click on the 'covariate tools. compute new/derived 2nd-level covariates' option
2) in the new gui, select the following options:
consider covariate QC_timeseries: raw values
summarize across timepoints: average
summarize across dimensions: do not aggregate
summarize across dimensions first: unchecked
condition-specific measures: checked
This will create two new second-level covariates for each condition, the first one will be QC_MeanGSchange (measure1) and the second QC_MeanMotion (measure2), each computed separately for each defined condition.
Similarly, in order to compute condition-specific QC_MaxGSchange and QC_MaxMotion measures, simply follow the same steps as above but now in the "summarize across timepoints" option select "maximum" instead of "average".
Hope this helps
Alfonso
Yes, to compute condition-specific QC_MeanGSchange and QC_MeanMotion measures you may:
1) go to the Setup.CovariatesFirstLevel tab, select the covariate named 'QC_timeseries' and click on the 'covariate tools. compute new/derived 2nd-level covariates' option
2) in the new gui, select the following options:
consider covariate QC_timeseries: raw values
summarize across timepoints: average
summarize across dimensions: do not aggregate
summarize across dimensions first: unchecked
condition-specific measures: checked
This will create two new second-level covariates for each condition, the first one will be QC_MeanGSchange (measure1) and the second QC_MeanMotion (measure2), each computed separately for each defined condition.
Similarly, in order to compute condition-specific QC_MaxGSchange and QC_MaxMotion measures, simply follow the same steps as above but now in the "summarize across timepoints" option select "maximum" instead of "average".
Hope this helps
Alfonso
Jan 25, 2019 06:01 PM | Daniel Westfall
RE: Multi-session pre-post design QC_ValidScans for each separate session
Thank you again!
Mar 6, 2019 10:03 PM | Jose Maximo
RE: Multi-session pre-post design QC_ValidScans for each separate session
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).
Hi Alfonso,
I have conn 18.a and am trying to compute QC_ValidScans for 3 different sessions, but when I try to use those parameters, I cannot use user-defined on "symmarize across timepoints". Is this a new update to conn? How would I be able to do this on 18.a?
Best,
Omar
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).
Hi Alfonso,
I have conn 18.a and am trying to compute QC_ValidScans for 3 different sessions, but when I try to use those parameters, I cannot use user-defined on "symmarize across timepoints". Is this a new update to conn? How would I be able to do this on 18.a?
Best,
Omar
Mar 7, 2019 12:03 PM | Alfonso Nieto-Castanon - Boston University
RE: Multi-session pre-post design QC_ValidScans for each separate session
Hi Omar,
Yes, sorry about that, the "user-defined" option mentioned in that thread had only been added in release 18b. Simply downloading/updating to the latest release in http://www.nitrc.org/projects/conn should fix that issue
Best
Alfonso
Originally posted by Jose Maximo:
Yes, sorry about that, the "user-defined" option mentioned in that thread had only been added in release 18b. Simply downloading/updating to the latest release in http://www.nitrc.org/projects/conn should fix that issue
Best
Alfonso
Originally posted by Jose Maximo:
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).
Hi Alfonso,
I have conn 18.a and am trying to compute QC_ValidScans for 3 different sessions, but when I try to use those parameters, I cannot use user-defined on "symmarize across timepoints". Is this a new update to conn? How would I be able to do this on 18.a?
Best,
Omar
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).
Hi Alfonso,
I have conn 18.a and am trying to compute QC_ValidScans for 3 different sessions, but when I try to use those parameters, I cannot use user-defined on "symmarize across timepoints". Is this a new update to conn? How would I be able to do this on 18.a?
Best,
Omar