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help > RE: How to transform a subset of MNI-space first-level maps to native space for each subject?
Jun 19, 2019 01:06 PM | Pravesh Parekh - National Institute of Mental Health and Neurosciences
RE: How to transform a subset of MNI-space first-level maps to native space for each subject?
Hi Stefan,
Can you tell me what did you specify in the bounding box and voxel size fields? Its usually best to let SPM figure out the correct bounding box by specifying Nan(2,3) in that field. Also, do mention the correct voxel size (the same size as your native space data). Finally, since you are transforming an atlas file, use the nearest neighbour interpolation method.
Best
Pravesh
Originally posted by Stefan Katletz:
Can you tell me what did you specify in the bounding box and voxel size fields? Its usually best to let SPM figure out the correct bounding box by specifying Nan(2,3) in that field. Also, do mention the correct voxel size (the same size as your native space data). Finally, since you are transforming an atlas file, use the nearest neighbour interpolation method.
Best
Pravesh
Originally posted by Stefan Katletz:
Hi,
I ran into the same problem, and no matter what I try, it doesn't seem to work in SPM12. Here is what I did:
1. T1 image segmented using "Segmentation" and the TPM.nii. Output is in native space, besides the c1-c5 maps I also generated the deformation fields (y_ and the inverse iy_).
2. When I use "Normalise (Write)" with a label map in MNI space (e.g. labels_Neuromorphometrics.nii) and the inverse deformation field, I end up with a volume which is not really registered with the original T1 image.
Can anybody point me to some recipe how to transform MNI to native space with the deformation fields from the segmentation process?
Thanks,
Stefan
Originally posted by Pravesh Parekh:
I ran into the same problem, and no matter what I try, it doesn't seem to work in SPM12. Here is what I did:
1. T1 image segmented using "Segmentation" and the TPM.nii. Output is in native space, besides the c1-c5 maps I also generated the deformation fields (y_ and the inverse iy_).
2. When I use "Normalise (Write)" with a label map in MNI space (e.g. labels_Neuromorphometrics.nii) and the inverse deformation field, I end up with a volume which is not really registered with the original T1 image.
Can anybody point me to some recipe how to transform MNI to native space with the deformation fields from the segmentation process?
Thanks,
Stefan
Originally posted by Pravesh Parekh:
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
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
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 | |