Dear Chris,

I found these files referring to an atlas that looks interesting to me under my MRIcron folder above, but contrary to the JHU white matter atlas, it is not available as a template from the MRIcron menu.

Could you please let me know which atlas this is (I presume it is another Johns Hopkins Uni atlas, but can't seem to find the details) and provide me with a reference for it so I can potentially use it?

Thanks very much in advance.

Best wishes,

Lukas

JHU_MNI_SS_BPM_TypeII_ver2.1
 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3358461/

I would contact the first author for more details. The rough notes I have for this are here:
  https://github.com/neurolabusc/NiiStat/blob/master/roi/read.me

The atlas has a single voxel that is clearly wrong, it is labelled as 'corticospinal tract right' but is located in the left hemisphere (at the boundary of PLIC_L and GP_L). When I next release the software I will relabel this voxel.

102|CST_R|corticospinal tract right|2
133|PLIC_L|posterior limb of internal capsule left|2
81|GP_L|globus pallidus left|1

Thanks a lot for the prompt and clear response Chris!

Best wishes,

Lukas

Hi again Chris,

Sorry having to bother you again!

When overlaying on the ch2better template in MRIcron, I noticed that it does not seem to be well-aligned with the MNI template (see attached screenshot).

This may be due to what I found in the README you sent me the GitHub link for: "Data warped to match stroke control dataset (ventricles larger and some cortical atrophy relative to young adults)".

Hence, I guess it would not be recommended to use this particular version of the atlas in studies on healthy adults?!

However, based on the readme I get the impression that there may also be an MNI space version of the atlas which is not warped to a stroke control dataset? Any idea how we could retrieve it?

I was also a little confused by the paper you sent as it compares different denoising pipelines but does not seem to be specifically mentioning the atlas?
Do you have any other references or contact info?

Thanks a lot in advance again!

Best wishes,

Lukas

As noted from the article where this image originated, the authors used SPM's segmentation-normalization
  https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3358461/
As noted when the MNI template was created, the algorithm used led to the template being larger than average. In contrast, SPM normalizes to an average sized brain. This can be seen nicely in Figure 1 of of Horn et al. (2017)
  https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6050588/
Therefore, if you used an MNI template for your normalization (FSL, ANTS) you would probably want to take this into account when using this template, as it is based on SPM normalization.

While I am happy that my MRIcron software has proved popular and robust, if your hardware can support it I would encourage you to try out MRIcroGL.
https://www.nitrc.org/projects/mricrogl
With MRIcroGL, if you choose the File/OpenStandard menu, you will see two templates: mni152 and spm152. The difference between these images is whether they use the larger MNI size or the more accurate SPM size.

You really want to choose your atlas to match your normalization procedures. In my own work with older stroke patients, I use templates that have larger ventricles to match the typical normalization seen for these people who are older than the sample used for the MNI dataset.

Thanks a ton again Chris, very informative!

I am already using MRIcroGL but had never noticed the choice between spm152 and mni152, nor did I know about this difference!

If I understand the last part of your message correctly, the JHU.nii file provided with MRIcron is simply normalized based on the spm instead of MNI template (thanks for that paper), but not adapted/normalized by your group for use in an elderly/stroke population, and can hence be used in any study where SPM normalization is done?

Best wishes,

Lukas