Hello,
This is the dataset that I am interested in analyzing as well. It seems like you guys are making great and speedy progress on the pediatric templates! I was wondering if I could be running fmriprep with the --anat-only argument in the meantime in order to use my time wisely and to save time for once the templates are released. If this were possible, would the template space be T1w or? What would be the easiest for fmriprep to pick up with for completing the functional pipelines with the pediatric templates?
Please let me know and thank you all for your time and efforts on this!
Hi @ajuliano
Thank you for your question. I think that would make sense for now running just the --anat-only. The template space would be defined in the outputs. The outputs are documented here: https://fmriprep.readthedocs.io/en/stable/outputs.html . I think fMRIPrep may be able to handle this task when your template has been added
Thank you for getting back to me! I guess my question is if I run fmriprep now using --anat-only and select the output space as T1w, would I need to repeat all of the freesurfer stages of the anatomical pipeline once the pediatric templates are available or can the T1w anatomical outputs be easily transformed into the pediatric template space from T1w space?
Since the freesurfer steps take the longest, I figured I would put the data to run the anatomical steps now, and then just put the functional steps to run once the pediatric templates become available. This would require fmriprep to do an additional transform on the files that get put into the anat subfolder of derivatives (for example, " anat/sub-<subject_label>_T1w_desc-preproc_T1w.nii.gz" would need to be transformed to " anat/sub-<subject_label>_[space-<pediatric-template-name>_]desc-preproc_T1w.nii.gz") before the functional pipeline is run so that output functional derivative files (i.e. func/sub-<subject_label>_[specifiers]_space-<space_label>_desc-preproc_bold.nii.gz) are in the pediatric template space and not T1w/subject native space. I’m was not sure if that would be possible or not.
I’m just curious if running fmriprep with --anat-only now would save me time in the long run. If it is the case that freesurfer would need to be re-run once the new templates become available, it would be better for me to wait. If fmriprep would be able to take the already run freesurfer T1w preproc output and quickly transform it into the new pediatric template space before running the functional pipelines, then I would start running the anatomical pipelines now.
Any thoughts on this or the logistics would be super helpful.
Hi @ajuliano
Thank you for your message. I looked further into this potential solution and found that it may be best to wait until the appropriate templates needed for your analysis are implemented. It is best to run fMRIPrep fully than piecewise. So it is best to wait for the moment. Templates are actively being added. What is the template you are interested in adding (if you may please provide a link too)? The process to add a template to fMRIPrep is currently being fleshed out. @rastko can provide more insights into this
I just wanted to note that version 1.4.1rc2 has been just posted and should allow brain extraction and spatial normalization using pediatric templates.
Also pinging @rastko since he was mentioned before.
This is so exciting! All of you just made my week.
Thank you guys so much for all of your hard work on this. I cannot even imagine.
They are having a lecture on the ABCD project at OHBM this Sunday, so this all just lines up so nicely.
Thank you again. Looking forward to downloading the version update!
Anthony
If you are attending OHBM we can meet up, just let us know.
Definitely would like to meet. My email is ajuliano@kesslerfoundation.org. Just let me know when is most convenient for you and I’ll switch around my schedule.