Hi there!

I am running a repeated measures (with 7 time points) resting-state functional connectivity analysis, and I am wondering which structural scan to use for each subject? Would it be better to take the average structural of the 7 sessions, or just use each subjects' first time point structural?

Any help would be greatly appreciated.

Thanks!

Hi Kaitlin,

Typically I would simply enter the first structural volume if I do not have any reason to expect between-session differences in the structural data. If you believe, on the other hand, that there may be structural differences between your sessions then it might be preferable to use session-specific structural volumes (and for that the simplest approach is probably to enter the different sessions as if they were different subjects, into the toolbox e.g. if you have 10 subjects then enter 70 as the number of subjects in Setup.Basic, and then when you get to the second-level analyses enter additional "within-subjects" second-level covariates to perform the desired repeated measure analyses; see for example this post for an example on how to do this http://www.nitrc.org/forum/message.php?m...)

Best
Alfonso

Originally posted by Kaitlin Cassady:

Hi Alfonso,

Thanks so much for the advice! I do have reason to believe that the structurals differ by session. I did read over the example that was posted, but I'm still not entirely sure what to use as my second-level covariate for my particular instance since there is only one subject group (16 subjects). Would would I use as my second-level covariate?

Thanks!
Kaitlin

Hi Alfonso,

Just thought of another question regarding this paradigm. If I were to enter 112 subjects (16 subjects x 7 sessions each) in order to enter all 112 structuruals, that would also automatically change the number of functionals and first-level covariates that I would need to enter. How would I go about this?

Thanks so much for all your help!
Kaitlin

Hi Kaitlin,

For multiple repeated measures the additional within-subject covariates needed will depend on the particular contrast (across your repeated measures) that you want to look at. For your 16 subjects and 7 sessions per subject (and assuming you entered first the 7 scans for the first subject, then the 7 scans for the second subject, etc.), if you are planning, for example, to use a contrast [-3 -2 -1 0 1 2 3] across sessions to look at the linear trends in connectivity across your 7 time-points, then you would define a new second-level covariate named "WithinSubject" and enter the values " kron(eye(16),null([-3 -2 -1 0 1 2 3])') " (without the quotes), and respond 'Yes' to the question of whether you want to expand this covariate into 96 new covariates. Then for your desired analyses simply select in the subject-effects list AllSubjects and these new 96 covariates named WithinSubject1 to WithinSubject96, and enter the between-subjects contrast "[1 zeros(1,96)]". That will implement the desired repeated-measures analysis (and you should double-check that the degrees of freedom of these analyses are 15, just to make sure everything was correctly defined). For different across time-point contrasts you would repeat this process simply changing the [-3 -2 -1 0 1 2 3] values above to your desired contrast. Another alternative way to perform these analyses (using a "pooled errors" approach instead of the CONN default "partitioned errors" approach) would be to take the connectivity maps into SPM and run a "flexible factorial" model, which will allow you to define your within-subject effects there. In any way, since all of these options are a bit cumbersome and your scenario is not that uncommon I will see if I can easily add the option to specify session-specific structural volumes into the next release of CONN (which should be out in a few days) to facilitate this form of analyses.

Hope this helps
Alfonso

Originally posted by Kaitlin Cassady:

Hi Alfonso,

Many thanks for all your help! I just downloaded the newest version of Conn (14p) and am exploring the new features. In regards to the "session-specific structural data" option for loading structural volumes, what would be the corresponding batch command for first declaring to use the "session-specific structural data" and then for loading in the volumes?

Thanks!
Kaitlin

Hi Kaitlin,

When using batch commands you do not need to explicitly define whether you will be using 'session-specific' or 'session-invariant' data, that is implicitly derived from the way you enter the corresponding files. In particular, when defining your structural data, if you use a single filename for each subject, such as:

  batch.Setup.structurals{1} = '/data/subject1/struct.img';
  batch.Setup.structurals{2} = '/data/subject2/struct.img';
  ...

those are interpreted to be session-invariant structural files (one file per subject), while if you use a list of filenames, such as:

  batch.Setup.structurals{1} = { '/data/subject1/session1/struct.img', '/data/subject1/session2/struct.img' };
  batch.Setup.structurals{2} = { '/data/subject2/session1/struct.img', '/data/subject2/session2/struct.img' };
  ...

those are interpreted to be session-specific (one file per session, for each subject).

Hope this helps
Alfonso


Originally posted by Kaitlin Cassady: