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help > RE: 2nd-level analysis
Jun 11, 2015 06:06 PM | Alfonso Nieto-Castanon - Boston University
RE: 2nd-level analysis
Hi Ben,
Regarding (1) yes, you are exactly correct, that contrast will test group x condition interactions in your data (typically for interactions one care about the two-sided results so remember to change the 'one-sided (positive)' option in the GUI to 'two-sided')
Regarding (2) and (3), if you want to do this manually you may select the BETA_Subject*_Condition*_Source*.nii files (these are the first-level fisher transformed connectivity maps for each subject/condition/source) and enter those into second-level anayses in SPM (see the FAQ for some additional info). Also, if you want, you can explore the SPM.mat files generated by CONN for each second-level analysis to perhaps more simply get the appropriate list of files needed (the field SPM.xY contains a list of all the first-level files included into your second-level CONN analyses and the field SPM.xX.X contains the associated second-level design matrix).
Hope this helps
Alfonso
Originally posted by Ben Xu:
Regarding (1) yes, you are exactly correct, that contrast will test group x condition interactions in your data (typically for interactions one care about the two-sided results so remember to change the 'one-sided (positive)' option in the GUI to 'two-sided')
Regarding (2) and (3), if you want to do this manually you may select the BETA_Subject*_Condition*_Source*.nii files (these are the first-level fisher transformed connectivity maps for each subject/condition/source) and enter those into second-level anayses in SPM (see the FAQ for some additional info). Also, if you want, you can explore the SPM.mat files generated by CONN for each second-level analysis to perhaps more simply get the appropriate list of files needed (the field SPM.xY contains a list of all the first-level files included into your second-level CONN analyses and the field SPM.xX.X contains the associated second-level design matrix).
Hope this helps
Alfonso
Originally posted by Ben Xu:
Hi,
I have two groups (exp and control) of resting state fMRI and each group has two conditions (pre and post intervention). I'd like to look at group x condition interaction at the 2nd-level analysis with one seed ROI. Here are my questions:
1. How do I set up the contrast at the 2nd level analysis? Is something like the following correct?
I selected "See-to_voxel" analysis. For "Between-subjects contrast" [1 -1], "Between-conditions contrast" [-1 1], and "Between-sources contrast" [1]
2. Is it possible to do some of the 2nd-level analyses in SPM8 or SPM12? If it is what kind of the 1st-level analysis files I should use?
3. This question is related to Question 2. There are several different types of output files (listed below) after the 1st-level analysis. What are these files? Where can I find the descriptions of these output files?
- BETA_*_source.nii
- corr_*_source.nii
- p_corr_*_source.nii
- pFDR_corr_*_source.nii
- Se_Subject*_Condition001.nii
Se_Subject*_Condition002.nii
Can I use any of these output files for 2nd-level contrasts in SPM?
Thanks much for your help.
Ben
I have two groups (exp and control) of resting state fMRI and each group has two conditions (pre and post intervention). I'd like to look at group x condition interaction at the 2nd-level analysis with one seed ROI. Here are my questions:
1. How do I set up the contrast at the 2nd level analysis? Is something like the following correct?
I selected "See-to_voxel" analysis. For "Between-subjects contrast" [1 -1], "Between-conditions contrast" [-1 1], and "Between-sources contrast" [1]
2. Is it possible to do some of the 2nd-level analyses in SPM8 or SPM12? If it is what kind of the 1st-level analysis files I should use?
3. This question is related to Question 2. There are several different types of output files (listed below) after the 1st-level analysis. What are these files? Where can I find the descriptions of these output files?
- BETA_*_source.nii
- corr_*_source.nii
- p_corr_*_source.nii
- pFDR_corr_*_source.nii
- Se_Subject*_Condition001.nii
Se_Subject*_Condition002.nii
Can I use any of these output files for 2nd-level contrasts in SPM?
Thanks much for your help.
Ben
Threaded View
| Title | Author | Date |
|---|---|---|
| Ben Xu | Jun 10, 2015 | |
| Alfonso Nieto-Castanon | Jun 11, 2015 | |
| Ben Xu | Jun 12, 2015 | |
| Alfonso Nieto-Castanon | Jun 12, 2015 | |
| Noah Philip | Jun 12, 2015 | |
| Alfonso Nieto-Castanon | Jun 12, 2015 | |
| Noah Philip | Jun 12, 2015 | |
| Ben Xu | Jun 15, 2015 | |