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help > RE: atlas.nii and networks.nii space
Nov 1, 2022 04:11 PM | Alfonso Nieto-Castanon - Boston University
RE: atlas.nii and networks.nii space
Hi Ryan,
My impression is that differences between MNI152 and MNI152Nlin are considerably smaller than the anatomical precision afforded by probabilistic or relatively large ROIs like those in atlas.nii and networks.nii ROIs, so it is perfectly fine to use those atlases in combination with fMRIPrep data or other data that has been normalized to MNI space, irrespective of the details of the methods/template used (SPM/FSL/etc.)
Special considerations may be needed in cases when we are interested, for example, in small subcortical regions, where differences between normalization templates and methods, and residual intersubject variability in its precise location after normalization, may be large compared to the ROI size. In those cases, subject-specific anatomical ROIs/labels might have the best chance of removing unwanted sources of anatomical variability (but lacking that, yes, fixed MNI-space ROIs that have been defined using precisely the same normalization procedure and templates as your functional data might help reduce at least some of those unwanted sources)
Best
Alfonso
Originally posted by ryanw412:
My impression is that differences between MNI152 and MNI152Nlin are considerably smaller than the anatomical precision afforded by probabilistic or relatively large ROIs like those in atlas.nii and networks.nii ROIs, so it is perfectly fine to use those atlases in combination with fMRIPrep data or other data that has been normalized to MNI space, irrespective of the details of the methods/template used (SPM/FSL/etc.)
Special considerations may be needed in cases when we are interested, for example, in small subcortical regions, where differences between normalization templates and methods, and residual intersubject variability in its precise location after normalization, may be large compared to the ROI size. In those cases, subject-specific anatomical ROIs/labels might have the best chance of removing unwanted sources of anatomical variability (but lacking that, yes, fixed MNI-space ROIs that have been defined using precisely the same normalization procedure and templates as your functional data might help reduce at least some of those unwanted sources)
Best
Alfonso
Originally posted by ryanw412:
Hello,
I recently learned that the atlas.nii and networks.nii that are preloaded with CONN are not in the same output space as fMRIprep's output space, which is MNI152NLin2009cAsym. Does this mean that I should not be using the atlas-based and network-based ROIs when running ROI-to-ROI analyses in CONN? Will I have to add my own ROIs that are in the correct space?
Thanks!
Best,
Ryan
I recently learned that the atlas.nii and networks.nii that are preloaded with CONN are not in the same output space as fMRIprep's output space, which is MNI152NLin2009cAsym. Does this mean that I should not be using the atlas-based and network-based ROIs when running ROI-to-ROI analyses in CONN? Will I have to add my own ROIs that are in the correct space?
Thanks!
Best,
Ryan
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| Title | Author | Date |
|---|---|---|
| ryanw412 | Oct 31, 2022 | |
| Alfonso Nieto-Castanon | Nov 1, 2022 | |