open-discussion
open-discussion > RE: CIFTI 2.0: a heads-up
Jul 7, 2013 02:07 PM | David Van Essen
RE: CIFTI 2.0: a heads-up
This posting responds to Drs. Ghosh and Daley, who appropriately
asked why the CIFTI format is based on NIFTI-2 rather than HDF5 and
whether this is a reversible decision.
The original decision made by the CIFTI working group in 2011 was based on several considerations and was made after considering HDF5 as an alternative.
NIFTI-1 is a widely accepted standard in the neuroimaging community and is supported by most brain imaging software platforms. However, NIFTI-1 was not suitable for the proposed CIFTI format primarily because it has a 16-bit limitation in the dimensions it supports (32,767 dimension length). In contrast, NIFTI-2 file header indices (adopted by the NIFTI committee in 2011) are 64-bit integers, allowing nearly unlimited dimension length. This modification made NIFTI-2 an attractive option for CIFTI because it met the core requirements, was substantially simpler to implement than HDF5, and offers an easier path for NIFTI-compliant and GIFTI-compliant brain imaging platforms to adopt.
The specific changes soon to be proposed for CIFTI 2.0 involve refinements and clarifications internal to the CIFTI XML metadata structure. The proposed changes would not be solved or simplified using an alternative format such as HDF5. NIFTI-2 remains an attractive format for CIFTI 2.0, as it provides the most straightforward path for ongoing CIFTI development.
We appreciate that HDF5 offers advantages when dealing with complex datasets that can capitalize on the rich hierarchical organization inherent in HDF5. If' the evolving data requirements for human structural and functional connectivity analyses would benefit strongly from HDF5, perhaps it might provide the substrate on which a future CIFTI 3.0 could be based. However, conversion to HDF5 would be a major undertaking, requiring group consensus on a wide range of format specifications needed to make implementation feasible. Hence, while it is important to remain genuinely open to this possibility in the future, HDF5 for CIFTI is not a route to be undertaken lightly.
David Van Essen, for the HCP software development team
The original decision made by the CIFTI working group in 2011 was based on several considerations and was made after considering HDF5 as an alternative.
NIFTI-1 is a widely accepted standard in the neuroimaging community and is supported by most brain imaging software platforms. However, NIFTI-1 was not suitable for the proposed CIFTI format primarily because it has a 16-bit limitation in the dimensions it supports (32,767 dimension length). In contrast, NIFTI-2 file header indices (adopted by the NIFTI committee in 2011) are 64-bit integers, allowing nearly unlimited dimension length. This modification made NIFTI-2 an attractive option for CIFTI because it met the core requirements, was substantially simpler to implement than HDF5, and offers an easier path for NIFTI-compliant and GIFTI-compliant brain imaging platforms to adopt.
The specific changes soon to be proposed for CIFTI 2.0 involve refinements and clarifications internal to the CIFTI XML metadata structure. The proposed changes would not be solved or simplified using an alternative format such as HDF5. NIFTI-2 remains an attractive format for CIFTI 2.0, as it provides the most straightforward path for ongoing CIFTI development.
We appreciate that HDF5 offers advantages when dealing with complex datasets that can capitalize on the rich hierarchical organization inherent in HDF5. If' the evolving data requirements for human structural and functional connectivity analyses would benefit strongly from HDF5, perhaps it might provide the substrate on which a future CIFTI 3.0 could be based. However, conversion to HDF5 would be a major undertaking, requiring group consensus on a wide range of format specifications needed to make implementation feasible. Hence, while it is important to remain genuinely open to this possibility in the future, HDF5 for CIFTI is not a route to be undertaken lightly.
David Van Essen, for the HCP software development team
Threaded View
Title | Author | Date |
---|---|---|
David Van Essen | Jul 1, 2013 | |
David Van Essen | Jul 7, 2013 | |
Satrajit Ghosh | Jul 2, 2013 | |
Mark Daley | Jul 2, 2013 | |