help
help > RE: Indirect corregistration, what exactly?
Sep 21, 2018 01:09 PM | Alfonso Nieto-Castanon - Boston University
RE: Indirect corregistration, what exactly?
Dear Daniel,
You are exactly right, you may simply apply the inverse "structural" normalization transformation to your normalized functional data. The precise deformation field file to use depends on your SPM version, it would be the *_seg_inv_sn.mat file for SPM8 or your iy_*.nii file for SPM12.
In general, in order to look at the details of the "indirect coregistration" step (or any other SPM-based preprocessing step in CONN), one simple trick in CONN is to go to the Functionals tab, select in the "functional tools" menu the option that reads "apply individual preprocessing step", then select your desired step (e.g. indirect coregistration), and then change the option that reads "run process and import results to CONN project" to "interactive SPM batch editor only (do not run process)". That, instead of actually running that preprocessing step, will take you to the standard SPM batch editor where you can read the precise sequence of steps that CONN is instructing SPM to do in order to implement the selected preprocessing step (the step that you care about is probably the second "normalize:write" step appearing in the module list there).
Hope this helps
Alfonso
Originally posted by Daniel Berge:
You are exactly right, you may simply apply the inverse "structural" normalization transformation to your normalized functional data. The precise deformation field file to use depends on your SPM version, it would be the *_seg_inv_sn.mat file for SPM8 or your iy_*.nii file for SPM12.
In general, in order to look at the details of the "indirect coregistration" step (or any other SPM-based preprocessing step in CONN), one simple trick in CONN is to go to the Functionals tab, select in the "functional tools" menu the option that reads "apply individual preprocessing step", then select your desired step (e.g. indirect coregistration), and then change the option that reads "run process and import results to CONN project" to "interactive SPM batch editor only (do not run process)". That, instead of actually running that preprocessing step, will take you to the standard SPM batch editor where you can read the precise sequence of steps that CONN is instructing SPM to do in order to implement the selected preprocessing step (the step that you care about is probably the second "normalize:write" step appearing in the module list there).
Hope this helps
Alfonso
Originally posted by Daniel Berge:
Dear conn developers,
First of all thanks for this amazing tool and for keeping this forum alive and extremely helpful.
Regarding the preprocessing steps, I found the "Indirect corregistration" very helpful to end up with functional to structural corregistration in subject space. As I already have my functional images normalised, as well as the structural ones (using direct normalization), I would like to skip some of the steps of this "indirect corregistration" pipeline. To do that, how is the last step done? I mean, is this simpy applying the inverse normalization transformation of the structural files to the normalized functional images ( I guess the iy.....)? Or is there something else that I am missing ( should I use the..seg8.mat file at some point?).
Thanks in advance.
Daniel Bergé
First of all thanks for this amazing tool and for keeping this forum alive and extremely helpful.
Regarding the preprocessing steps, I found the "Indirect corregistration" very helpful to end up with functional to structural corregistration in subject space. As I already have my functional images normalised, as well as the structural ones (using direct normalization), I would like to skip some of the steps of this "indirect corregistration" pipeline. To do that, how is the last step done? I mean, is this simpy applying the inverse normalization transformation of the structural files to the normalized functional images ( I guess the iy.....)? Or is there something else that I am missing ( should I use the..seg8.mat file at some point?).
Thanks in advance.
Daniel Bergé
Threaded View
| Title | Author | Date |
|---|---|---|
| Daniel Berge | Sep 18, 2018 | |
| Alfonso Nieto-Castanon | Sep 21, 2018 | |