I am looking for a subcortical atlas that can be used with the MNI152NLin2009cAsym template (default of fmriprep). I found a parcellation file from the fmriprep image named /niworkflows_data/mni_icbm152_nlin_asym_09c/1mm_parc.nii.gz, and I guess it was converted from the Harvard Oxford Atlas in FSL based on the scripts from the same folder.
I have two questions:
Is that parcellation file also in the MNI152NLin2009cAsym template space (instead of the MNI152 6th used by FSL)?
Is there any associated file that can map numbers in that file to label names?
Did you find the atlas for MNI152Nlin2009cAsym? I am looking for a parcelled atlas for the symetric version. Please any help would be really appreciated.
We are working on this issue right now. Please check on the development of our templateflow project (https://github.com/templateflow/). We will be adding all the templates available to fmriprep there, including mappings of segmentations, parcellations and surfaces between them. I’ll be posting a preprint ASAP.
Regarding the two questions from @feilong (sorry for the huge delay in answering, this is probably useless to you at this point but will leave this here for people asking about it):
No, that parcellation corresponds to the MNI152 6th generation. We only regridded it to match MNI152NLin2009cAsym.
No, but as you mention that was done using the Harvard Oxford Atlas and the labels were mapped as in the scripts you already accessed.
With templateflow we will be addressing both two questions (which are extremely relevant, that must be said). Hopefully I can post updates here soon.
The problem is that Harvard atlases were produced with the MNI152 Linear version of the MNI templates. Although the MNI152Nlin2009cAsym is well aligned with the linear version, there will always be inconsistencies between atlases if they would have defined using the MNI152Nlin2009cAsym template as well.
In summary, by applying an atlas defined w.r.t. the Linear version of MNI152 on data aligned to MNI152Nlin2009cAsym you are dismissing some accuracy errors derived from the differences between templates.
Then you would think, why didn’t you use MNI152 linear as the registration target in the first place? The answer is that then you would be introducing similar accuracy errors but on your registration step. We considered that it was more important to have the best alignment possible to the standard space, assuming that the current lack of atlases defined on MNI152Nlin2009cAsym would be addressed at some point in time.
For these reasons, we are working on an easy way of transferring atlas information through different templates. That would be one of the objectives of the project I mentioned above (templateflow).
After almost 2 years, I can give a proper solution to this question.
We have just uploaded two parcellations (Harvard-Oxford and Schaefer2018) to TemplateFlow, in their original FSL MNI space (or MNI152NLin6Asym) and corresponding resamplings in MNI152NLin2009cAsym. The transform I used to perform this mapping was estimated with the TemplateFlow registration framework and it is also available via TemplateFlow.
The associated files are under the MNI152NLin6Asym template, although I’ll try to generate more metadata for the Schaefer2018 atlas during a few more days.
Is the Harvard-Oxford atlas still supposed to be in MNI152NLin2009cAsym space in templateflow? I downloaded templateflow, but cannot find this atlas in this space. It is possible that I installed it incorrectly.
Those commands run for me, and when I run the final one, I get a nibabel Nifti1Image object. It still doesn’t look like I have the Harvard-Oxford atlas, though.
Thanks @oesteban ! It seems the TemplateFlow registration framework can be conveniently used as a Docker image. I wonder if there is a pre-built Docker image for it somewhere on DockerHub?
I’ve read all posts regarding this topic at length but still have a lingering question… If an fMRIPrep preprocessed dataset had --output-spaces set to the defaulted MNI152NLin2009cAsym template (thus, no :res stated), which MNI152NLin2009cAsym based Harvard Oxford Atlas would you use from the templateflow, res-1 or res-2?
Apologies if the answer is obvious or previously addressed!
Phoenix
One way, if not redoing fMRIPrep, might be to resampling the atlas.
P.S. I am very new to this; thus, there might be a myriad of other options I am not aware of!
Which is the native resolution of your images that is outputted by fmriprep?
Of note, for MNI152NLin2009c, res-1 is 1mm iso, res-2 is 2mm iso.
If your native resolution is higher (i.e. voxel size smaller) than res-2, I would resample the atlas from res-1 to your native resolution that is outputted by fmriprep.
If your native resolution is smaller (i.e. voxel size bigger) than res-2, I would resample the atlas from res-2 to your native resolution that is outputted by fmriprep.
But I guess the reversed choice would be somewhat very close.
Thank you both for your helpful responses. Generally, how do the atlases work? Per instruction by my PI, I’ve resampled the func data to 2x2x2 and downloaded the corresponding standard image and atlas from the templateflow. I’ve uploaded both to fsleyes but how do I know what regions are what without using the HOC and HOS atlases provided by FSLeyes (which are not based on the MNI152NLin2009cAsym)? If I use these FSLeyes atlases to identify regions, it notifies me that they’re not the same resolution (obviously), which makes me reluctant to base my masks off these labels.
I am not expert with atlases but from what I saw, the different regions from the atlas have different indexes (1, 2, 3…). The atlas are provided with a table that show the correspondance between this index and the name of the associated region.
For exemple, let’s assume you plan to use the Schaefer2018 atlas (200 Parcels 17 Networks) : in templateflow, you get this correspondance in the file: tpl-MNI152NLin2009cAsym_atlas-Schaefer2018_desc-200Parcels17Networks_dseg.tsv
I appreciate your help regardless, and thank you for bringing the .tsv files to my attention. My only confusion now is that there aren’t ones for HO atlases.
Ho, I see. Indeed I cannot see any tsv file corresponding to this atlas for tpl-MNI152NLin2009cAsym in templateflow.
However I can see 3 files:
tpl-MNI152NLin6Asym_atlas-HOCPA_dseg.tsv
tpl-MNI152NLin6Asym_atlas-HOCPAL_dseg.tsv
tpl-MNI152NLin6Asym_atlas-HOSPA_dseg.tsv
in the tpl-MNI152NLin6Asym folder that should help you. One should write similar ones for tpl-MNI152NLin2009cAsym to not confuse people using this atlas.
