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help > RE: How to transform a subset of MNI-space first-level maps to native space for each subject?
Aug 3, 2018 12:08 PM | Pravesh Parekh - University of Oslo
RE: How to transform a subset of MNI-space first-level maps to native space for each subject?
Hi,
A usual rule of thumb for converting data from MNI space to native space is to use the inverse deformation field. When performing the segmentation steps, SPM will write out the forward and the reverse deformation fields (by default they are turned off; you need to select whether you want to save them or not). When running the preprocessing steps in Conn, Conn saves both these fields for you (the forward deformation is the y_*.nii and the inverse deformation is the iy_*.nii file).
You can run the normalization step (Normalize: Write) in SPM and specify the deformation field as the iy_*.nii file and select the images in MNI space (that you want to convert to native space) as the images that you want to write. Be sure to specify the correct values for voxel size and the bounding box (as per your native space file). If you set the bounding box to NaN(2,3), SPM will figure it out from the specified deformation field.
Hope that helps
Best
Pravesh
Originally posted by fred Sampedro:
A usual rule of thumb for converting data from MNI space to native space is to use the inverse deformation field. When performing the segmentation steps, SPM will write out the forward and the reverse deformation fields (by default they are turned off; you need to select whether you want to save them or not). When running the preprocessing steps in Conn, Conn saves both these fields for you (the forward deformation is the y_*.nii and the inverse deformation is the iy_*.nii file).
You can run the normalization step (Normalize: Write) in SPM and specify the deformation field as the iy_*.nii file and select the images in MNI space (that you want to convert to native space) as the images that you want to write. Be sure to specify the correct values for voxel size and the bounding box (as per your native space file). If you set the bounding box to NaN(2,3), SPM will figure it out from the specified deformation field.
Hope that helps
Best
Pravesh
Originally posted by fred Sampedro:
Dear CONN experts,
I have preprocessed all my subjects in CONN v18 in MNI space. Now, I would like to convert the resulting MNI-space seed-to-voxel and ICA maps for each subject to native space, in order to subsequently co-register them with their associated structural T1MRI images and compute some specific properties on hand-drawn ROIs (specific to each subject). I am aware that CONN allows to do the preprocessing in native space, but I would like to avoid doing this if possible.
Could you please guide me on finding the appropriate SPM12 commands to convert the CONN first-level MNI-space maps to native-space for each subject?
Thanks a lot!
I have preprocessed all my subjects in CONN v18 in MNI space. Now, I would like to convert the resulting MNI-space seed-to-voxel and ICA maps for each subject to native space, in order to subsequently co-register them with their associated structural T1MRI images and compute some specific properties on hand-drawn ROIs (specific to each subject). I am aware that CONN allows to do the preprocessing in native space, but I would like to avoid doing this if possible.
Could you please guide me on finding the appropriate SPM12 commands to convert the CONN first-level MNI-space maps to native-space for each subject?
Thanks a lot!
Threaded View
| Title | Author | Date |
|---|---|---|
| fred Sampedro | Aug 3, 2018 | |
| Pravesh Parekh | Aug 3, 2018 | |
| Stefan Katletz | Jun 19, 2019 | |
| Pravesh Parekh | Jun 19, 2019 | |
| Stefan Katletz | Jun 21, 2019 | |
| Stefan Katletz | Jun 21, 2019 | |
| Stefan Katletz | Jun 21, 2019 | |
| Pravesh Parekh | Jun 24, 2019 | |
| Stefan Katletz | Jun 25, 2019 | |