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help > RE: How to transform a subset of MNI-space first-level maps to native space for each subject?
Jun 25, 2019 12:06 PM | Stefan Katletz
RE: How to transform a subset of MNI-space first-level maps to native space for each subject?
Hi Pravesh,
I used the images (TPM and labels_Neuromorphometrics) from spm12 (tpm folder). I redid all my steps to find out what is going wrong and I think I found the culprit.
It seems that when I change the header of labels_Neuromorphometrics (Statistics/Intention -> Labels, Optional/Regular -> 98, then save header in order to see the label names in the overlay) the volume is slightly shifted. I did this before the un-normalization, which made the effect even worse. Changing the header after un-normalization, the shift is also noticable but not so bad.
Without modifying the header the match is near perfect. Is this a bug in mricron? After all, I didn't change the values in the Dimensions or Reorient tabs.
Stefan
Originally posted by Pravesh Parekh:
I used the images (TPM and labels_Neuromorphometrics) from spm12 (tpm folder). I redid all my steps to find out what is going wrong and I think I found the culprit.
It seems that when I change the header of labels_Neuromorphometrics (Statistics/Intention -> Labels, Optional/Regular -> 98, then save header in order to see the label names in the overlay) the volume is slightly shifted. I did this before the un-normalization, which made the effect even worse. Changing the header after un-normalization, the shift is also noticable but not so bad.
Without modifying the header the match is near perfect. Is this a bug in mricron? After all, I didn't change the values in the Dimensions or Reorient tabs.
Stefan
Originally posted by Pravesh Parekh:
Hi
Stefan,
The TPM and labels_Neuromorphometrics images are both in the MNI space and are aligned to each other. Something seems to be wrong with the overlay screenshot that you shared. Are you using the same TPM that comes with SPM (12?) or is this some custom TPM? I just segmented a T1w image and passed the inverse deformation field to the normalization step; the resulting un-normalized (native space) labels_Neuromorphometrics image looks absolutely fine and is perfectly aligned too. If its not working out for you, perhaps you could share your T1w image?
Best
Pravesh
Originally posted by Stefan Katletz:
The TPM and labels_Neuromorphometrics images are both in the MNI space and are aligned to each other. Something seems to be wrong with the overlay screenshot that you shared. Are you using the same TPM that comes with SPM (12?) or is this some custom TPM? I just segmented a T1w image and passed the inverse deformation field to the normalization step; the resulting un-normalized (native space) labels_Neuromorphometrics image looks absolutely fine and is perfectly aligned too. If its not working out for you, perhaps you could share your T1w image?
Best
Pravesh
Originally posted by Stefan Katletz:
Here is the finally labeled brain in natvie
space.
Thanks for sharing the instructions.
Stefan
Thanks for sharing the instructions.
Stefan
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 | |