Older adult MNI template

Is it possible to add the older adult MNI MRI template discussed here https://www.ncbi.nlm.nih.gov/pubmed/22440645 to fmriprep? Nii format file comes with the following clinical toolbox: https://www.nitrc.org/projects/clinicaltbx/
Thank you,
Jeremy

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As one of the authors behind the clinical toolbox, I would be delighted if people used my work and cited my paper. However, users should be aware that the template developed by Rorden et al. (2012) was specifically designed for use with SPM. While generally ignored, it should be noted that SPM tends to generate average sized brains, while tools like FSL and ANTs come with templates that are MNI template sized. The MNI template is larger than average. As noted when the template was released, this was a side-effect of the algorithm used to develop this template (there is no evidence that people in Montreal have larger than average brains). This difference is best seen in Figure 1 of Horn et al. (2017). This difference explains why MRIcroGL’s File/OpenStandard menu lists mni152 as well as spm152. The former template is for images normalized to MNI sized brains, while the latter is for average sized brains.

As you note, human brain volume shrinks on average about 5% for each decade after 40. Therefore, it might be worthwhile using an older template.

I really do not know how the regularization tuning influences different tools. I do know the images developed by Rorden et al were intentionally designed to work hand in glove with SPM. For more general algorithms, I suspect there are better options, e.g. those from John E. Richards

This is great input. Thanks so much Chris! Given this, it does seem better to have these older adult templates added as an option in fmriprep instead.

Hi @Jeremy_Purcell, I have added https://github.com/templateflow/templateflow/issues/19 with your request.

@Chris_Rorden, do you happen to remember the license of the template and whether it would allow us to redistribute it (of course requesting the citation of whatever works need be referenced).

I have a set of average MRI templates. Range in age from 2 weeks through 89 years, in 3 mo, 6 mo, half year, or five year intervals. I would be glad to have someone add them to the fmriprep processing. The avg templates are hosted on NITRC under neurodevelopmental mri database, group is neurodev. Chris referenced my www site that has info. John

Thanks, do you know when this template will be added? I am interested in using it for my current data analysis…

@John_Richards I have just requested to join your NITRC team

Hi there!

I am also very much interested in using an older adult template for my analysis. I am actually investigating a study cohort made up of older adults, and individuals with mild cognitive impairments and Alzheimer’s disease, and so a template made from this cohort would be even better, if possible.

I just wanted to double-check that the only way in order to use custom templates which are not yet available, is that we would need to upload them to tensorflow and allow them for shared public usage? Currently, is there is no function within fmriprep which allows users to use templates that are stored locally/privately? With our study protocols, I am unsure whether our data can be uploaded and shared publicly due to our ethics.

You can your custom templates without sharing (or uploading anywhere). Just add your template to the TemplateFlow (not tensorflow) home directory. Check Python Client - TemplateFlow docs.

Once your template is indexed by TemplateFlow, you just pass your template name with the --output-spaces argument (e.g., --output-spaces MyCustomTemplateName).

A custom template is not identifiable data, so very unlikely sharing it would be that cumbersome. But yes, you should definitely see whether you can publish derived data under a local ethics approval.

These templates are not publicly available, so the only way for you is to proceed to the NITRC page and fill in all the required information, get approved by the owner of the team, download the data, re-structure it following TemplateFlow’s guidelines and then add it as a custom template as I mentioned above.

Alternatively, someone could upload Chris’ template (acknowledging the problems he mentioned in his post) to TemplateFlow. Unfortunately, I don’t have the bandwidth to do this right now.

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Thanks so much!

I installed templateflow and changed the path of the environment variable, $TEMPLATEFLOW_HOME. I have added my custom template into the templateflow directory and specified the output space as --output-spaces DPRCcustom. However upon running fmriprep, I get an error saying that the ‘tpl prefix’ is required, but have made sure to include the tpl- prefix on the folder and file name. My custom template directory looks like this:

$TEMPLATEFLOW_HOME/
    tpl-DPRCcustom/
        template_description.json
        tpl-DPRCcustom_T1w.nii.gz

I am unsure of what the problem is, and would appreciate any input, thanks!

  1. How are you running fMRIPrep? (or more precisely, are you using containers? and what is the command line?
  2. I believe fMRIPrep requires your template to have a corresponding brain mask (probabilistic or binary, I think the former has more priority).