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TemplateFlow Archive

RRID:SCR_021876 Update Archive

This repository corresponds to the DataLad super-dataset of the TemplateFlow infrastructure. Therefore, this repository indexes actual template datasets (Git repositories), that are linked as Git submodules. This repository is the right place to send issues affecting the whole infrastructure. It is automatically managed via GitHub Actions.

About

Reference anatomies of the brain and corresponding atlases play a central role in experimental neuroimaging workflows and are the foundation for reporting standardized results. The choice of such references —i.e., templates— and atlases is one relevant source of methodological variability across studies, which has recently been brought to attention as an important challenge to reproducibility in neuroscience. TemplateFlow is a publicly available framework for human and nonhuman brain models. The framework combines an open database with software for access, management, and vetting, allowing scientists to distribute their resources under FAIR —findable, accessible, interoperable, reusable— principles. TemplateFlow supports a multifaceted insight into brains across species, and enables multiverse analyses testing whether results generalize across standard references, scales, and in the long term, species, thereby contributing to increasing the reliability of neuroimaging results.

Please visit www.templateflow.org for a more comprehensive description of this project. News and some discussions take place at the Nipy discourse platform.

Vision

The rationale behind TemplateFlow and how we envision it as a fundamental instrument to neuroimaging studies is presented in our preprint:

Ciric R. et al., 2021. doi:10.1101/2021.02.10.430678

Acknowledgments

This work is steered and maintained by the NiPreps Community. The development of this framework is supported the NIMH (RF1MH121867, RAP, OE).

Thanks to the DataLad developers, as we rely on their wonderful tool for the management of the TemplateFlow Archive.

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tpl-mni152nlin6asym's Issues

High resolution for "low" resolution versions of the MNI152NLin6Asym template?

Some of the low resolutions versions of the MNI152NLin6Asym template are actually high resolution. Or am I misinterpreting the meaning of the "res-0X" part?

This can lead to unexpected results in software that uses template flow; e.g. in fmriprep, upsampling of resting-state fMRI scans to 0.5 mm isotropic resolution when an output of 3 mm isotropic resolution was expected.

pixdim1		0.500000	pixdim2		0.500000	pixdim3		0.500000	pixdim4		1.000000		./tpl-MNI152NLin6Asym/tpl-MNI152NLin6Asym_res-03_T1w.nii.gz
pixdim1		0.700000	pixdim2		0.700000	pixdim3		0.700000	pixdim4		1.000000		./tpl-MNI152NLin6Asym/tpl-MNI152NLin6Asym_res-04_T2w.nii.gz
pixdim1		0.700000	pixdim2		0.700000	pixdim3		0.700000	pixdim4		1.000000		./tpl-MNI152NLin6Asym/tpl-MNI152NLin6Asym_res-04_T1w.nii.gz
pixdim1		0.700000	pixdim2		0.700000	pixdim3		0.700000	pixdim4		1.000000		./tpl-MNI152NLin6Asym/tpl-MNI152NLin6Asym_res-04_desc-brain_T1w.nii.gz
pixdim1		0.700000	pixdim2		0.700000	pixdim3		0.700000	pixdim4		1.000000		./tpl-MNI152NLin6Asym/tpl-MNI152NLin6Asym_res-04_desc-brain_mask.nii.gz
pixdim1		0.700000	pixdim2		0.700000	pixdim3		0.700000	pixdim4		1.000000		./tpl-MNI152NLin6Asym/tpl-MNI152NLin6Asym_res-04_desc-brain_T2w.nii.gz
pixdim1		0.800000	pixdim2		0.800000	pixdim3		0.800000	pixdim4		1.000000		./tpl-MNI152NLin6Asym/tpl-MNI152NLin6Asym_res-05_desc-brain_T1w.nii.gz
pixdim1		0.800000	pixdim2		0.800000	pixdim3		0.800000	pixdim4		1.000000		./tpl-MNI152NLin6Asym/tpl-MNI152NLin6Asym_res-05_desc-brain_T2w.nii.gz
pixdim1		0.800000	pixdim2		0.800000	pixdim3		0.800000	pixdim4		1.000000		./tpl-MNI152NLin6Asym/tpl-MNI152NLin6Asym_res-05_T2w.nii.gz
pixdim1		0.800000	pixdim2		0.800000	pixdim3		0.800000	pixdim4		1.000000		./tpl-MNI152NLin6Asym/tpl-MNI152NLin6Asym_res-05_T1w.nii.gz
pixdim1		0.800000	pixdim2		0.800000	pixdim3		0.800000	pixdim4		1.000000		./tpl-MNI152NLin6Asym/tpl-MNI152NLin6Asym_res-05_desc-brain_mask.nii.gz
pixdim1		1.600000	pixdim2		1.600000	pixdim3		1.600000	pixdim4		0.000000		./tpl-MNI152NLin6Asym/tpl-MNI152NLin6Asym_res-06_atlas-HCP_dseg.nii.gz

3mm Resolution Template has 0.5mm Resolution

I'm not sure if this is the right place to post this, but when I download the 3mm MNI152NLin6Asym template the spacing is actually 0.5 mm instead of 3mm.

I even tried downloading it directly from AWS:
https://templateflow.s3.amazonaws.com/tpl-MNI152NLin6Asym/tpl-MNI152NLin6Asym_res-03_T1w.nii.gz

Output from fslinfo:

data_type INT16
dim1 364
dim2 436
dim3 364
dim4 1
datatype 4
pixdim1 0.500000
pixdim2 0.500000
pixdim3 0.500000
pixdim4 1.000000
cal_max 250.000000
cal_min 0.000000
file_type NIFTI-1+

I assume this is some sort of mistake, but let me know I'm wrong and I just don't understand how the templateflow resolutions work.

Missing info from HOSPA atlas

So I have noticed 3 issues regarding the HOSPA in the _dseg.tsv file.

  1. The dseg.tsv file is missing from: MNI152NLin2009cAsym

  2. The brainstem is missing in the _dseg file in MNI152NLin6Asym link. It currently reads:

6 	Left Pallidum 	54, 62, 35
8 	Left Hippocampus 	59, 54, 27

The brainstem is included in the nifti image.

  1. Finally the index of the dseg starts at zero, but here (and in most atlases) the indexing starts at 1 in the image files. This could lead to greater confusion (for example the brainstem has a value 8 in the nifti file). While the xyz coordinates could be used to find the actual value, perhaps an additional column in the data for this information should be added? (Suggested column name: value)

I can PR a fix for all three of these things unless any of these are meant to be the case.

What is the Schaefer parcellation version?

I noticed that the Schaefer parcellations were added over a year ago. Are they the originally published parcellations?

The labels and the parcellation were updated recently. I don't think the parcel identities changed but parcel to Yeo network assignments were updated at one point.
https://github.com/ThomasYeoLab/CBIG/releases/tag/v0.14.3-Update_Yeo2011_Schaefer2018_labelname
https://github.com/ThomasYeoLab/CBIG/releases/tag/v0.10.2-Schaefer2018_LocalGlobal
and fixes to HCP cifti compatibility in the most recent.
https://github.com/ThomasYeoLab/CBIG/releases/tag/v0.17.1-Schaefer2018_LocalGlobal

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