Dear AFNI experts,
I am attempting to download an anatomical mask on MNI space, Could you give me some suggestions?
I tried this command:
whereami -prefix lba41mask -mask_atlas_region ‘TT_Daemon::Left Brodmann 41’
3dresample -dxyz 3.0 3.0 3.0 -prefix LBA41 -inset lba41mask+tlrc
But when I tried to extract the time series, the time file was empty.
The warning was that input and mask datasets are not the same dimensions (as attached)
Dan
The Talairach daemon is in Talairach space, of course, and not in MNI space. If you do want to use it in MNI space, then you might want to consider using a method to transform the dataset to Talairach space, as in our previous thread using 3dfractionize.
If you do want to use this atlas in its native space, you would change the 3dresample command to have a -master of the dataset that you want to mask, instead of using the -dxyz option.
The Talairach daemon atlas, however, has several issues. First, it has no template available, so the TT_N27 dataset does not align particularly well with it. Consequently, all transformations (3dfractionize uses a specific warp between an MNI N27 and TT N27) provide only a very approximate transformation. The atlas was done for a specific person with no available image data. Secondly, the atlas is very coarse with 5mm spacing between slices. Thirdly, the digitized version of the atlas both introduces and exposes various errors - cross slice discontinuities and outright digitizing mistakes. Finally, the Brodmann regions, in particular, are drawn very finely on cortical boundaries that typically lie outside the brain even in Talairached datasets, making alignment overlap difficult So while we provide this atlas because of its historical importance in AFNI and to the general neuroscience community, it is not recommended.
One of the main advantages of the Talairach atlas is its Brodmann regions, that are only partially described in other atlases. I do have an alpha version of a Brodmann atlas stored in the link below. This was developed by Juergen Mai and Milan Matajnik. I believe this provides a much better mapping of the Brodmann regions. These are in the MNI 2009c asymmetric space, projected from the MNI 2009c cortical surfaces into the cortical ribbon mask.
Thank you very much！
Hi Mr, Glen,
Per your comment regarding TT Daemon not aligning well with TT_27, I have certainly noticed this (See first image). However when extracting similar regions from the Brodmann_MM atlas recommended in this old thread I am finding same issue with BA22 having sections WAY outside the brain (see second image).
Is this to be expected, ie. always an issue of TT vs MNI atlas alignment issues? Something else?
~Dane
The MNI space is larger and shifted away from Talairach space. The MNI 2009c template is also different than the N27 dataset in MNI space, so the regions that correspond to MNI 2009c template space are not going to have direct x,y,z correspondence to TT_N27 space. If you look at the same region on the MNI 2009c space, it’s much more sensible. Still we have found that region specifically has a known problem and needs some correction by the authors. The posterior end of the region goes too far superior. We are waiting for that correction. In the meantime, you might consider the similar regions in the MNI HCP Glasser atlas and the Brainnetome atlas. Both of those atlases show regions similar to BA22 as two separate regions.
Hello Daniel,
Sorry to jump on this subject.
I was actually looking for a human 3D Brodmann atlas. Do you think that I can use that one (https://afni.nimh.nih.gov/pub/dist/atlases/Brodmann_MM/) for publication?
Is there a publication that I can read/site associated with this atlas?
By any chance, do you know an atlas that I can use to complete this one with subcortical, brainstem and cerebellum regions?
Thank you!
Clément
Sincerely appreciate the information Mr. Glen. Unfortunately as seen in attached both Brainnetomme and Glasser have the same problem with the STG areas completely outside the N27 brain (as seen below). This brings a few questions to help me plot a way forward:
Does utilizing MNI atlases for ROI really require registering all functionals to an MNI 2009c anatomical then?
1b. What is efficacy then of re-registering functionals to a MNI after already doing so to TT27 tlrc space? Seems problematic doing two such translations vs. going back to scratch and starting in MNI space.
How does one locate an appropriate anatomical seed area in tlrc space on a N27 registered volume for with reasonable confidence?
~Dane
Hi, Dane-
When you think of an atlas, you can never think of it in isolation. It is always tied to a particular space, or more specifically template.
The standard Brainnetome and Glasser atlases can only be overlaid and used on the MNI template (probably specifically the MNI 2009c, as you note, because “MNI” has become a family of spaces, grids and templates).
The voxel dimensions and matrix dimensions of the Brainnetome and MNI_Glasser* atlases appear to be:
$ 3dinfo -ad3 -n4 -prefix BN_Atlas_246_1mm.nii.gz MNI_Glasser_HCP_v1.0.nii.gz
1.000000 1.000000 1.000000 182 218 182 1 BN_Atlas_246_1mm.nii.gz
1.000000 1.000000 1.000000 256 256 256 1 MNI_Glasser_HCP_v1.0.nii.gz
The Glasser atlas matches the MNI template well, but the grid dimensions are a bit different than MNI2009c. To make it match better the @SSwarper base volume MNI, I once ran:
3dZeropad -master MNI152_2009_template_SSW.nii.gz -prefix MNI_Glasser_HCP_v1.0_LPI_2009c.nii.gz MNI_Glasser_HCP_v1.0_LPI.nii.gz
3drefit -copytables MNI_Glasser_HCP_v1.0.nii.gz MNI_Glasser_HCP_v1.0_LPI_2009c.nii.gz
3drefit -cmap INT_CMAP MNI_Glasser_HCP_v1.0_LPI_2009c.nii.gz
… where the 3drefits are to copy of the labeltables and then to make the default colorbar be "integer"y, respectively.
The BN_Atlas_246_1mm.nii.gz appears to mostly match the MNI2009c well, but at the edges it seems a bit “rounded in”, oddly.
Re. Q1) Yes.
Re. Q2) It would be non-optimal re warp all functionals from TT27 space to MNI space, because they have already been re-gridded once from their native space, and warping them all again would smooth them additionally. It would be better to use the appropriate MNI template as a reference base for the dsets directly (e.g., make it the template base in @SSwarper for skullstripping and nonlinear warping and then providing that info to afni_proc.py).
Re. Q3) One would want to have a good atlas in that TT27 template space. Offhand, I don’t know of one (Daniel might?).
→ One could warp one of the MNI templates to TT27 space, and then use it there. One will have to do a bit of regridding and ROI smoothing; that might be better than warping the TT27 space EPI data to MNI, because the ROI voxels are smaller.
–pt
Dear Prof.Glen,
Thanks for your greatly useful answer, are there any reference paper of this brodmann atlas in MNI space by Juergen Mai and Milan Matajnik? Only one related book was found.
Best wishes,
Peng
I think the 2016 book form is the original source of the dataset.
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