AAL2 atlas labels

[14thibea]

Hello @faskowit,

Thanks a lot for this wonderful repo!
I already used aicha with freesurfer recon-all and everything went smoothly, and I am now trying to use the aal atlas (corresponding to AAL2?) you put on this repo.
However, I am not sure how to link the regions of your version (LH_region_1, LH_region_2...) to the ones of the original atlas (Precentral_L, Frontal_Sup_2_L...). Is there a dictionary somewhere to give an equivalence between them?

[faskowit]

Hi! Thanks for your interest in this repo! For the AAL, I unfortunately do not have a mapping to the original labeling scheme, and it would be a bunch of work to figure out the mapping and to make sure it is correct. Therefore, if the names of the labels are critical, I am afraid that you'll have to use the MNI version of the AAL atlas and find a method to warp the MNI to your individual subjects

[Sleosoz]

Hi, I second the compliments on this repo!! It would indeed be very helpful to count on a mapping to the original region names for the AAL, Arslan, and Power atlases. Is it still not possible to count on those in this repo? Thanks in advance!

[faskowit]

Hi! Thanks again for the compliments and your interest in the tools! But unfortunately, the situation is the same as before... I don't have the bandwidth to assign the regions better, more cognitive/behavioral relevant names. However, I do have a suggestion about how to hack it reasonably, if you would like to do this.

If you fit the AAL labels, for example, with maTT or maTT2 you get a nice cortical ribbon with numbered labels. Then, you could also do a quick and dirty volumetric nonlinear warp using a tool like ANTs, FNIRT, or DARTEL of the Yeo/Scheafer/Yan labels (which have nice, relevant names) in MNI space to the subject space. Then, for each numbered region of the cortical AAL, you could identify the Yeo/Schaefer/Yan node with the greatest voxel overlap in subject space. I think this would be a reasonable way to give names to the regions!

[FrancisOWO]

Hello @faskowit ,

Thanks for your great repo!
I have performed a surface-based visualization of this AAL atlas (41x2 regions) based on the region mapping provided in this comment from the ggsegAal repo. The regions listed by the commenter are derived from the AAL2 atlas. My visualization result and the corresponding R source code can be found in the latest comment.

Since I don’t have a background in neuroscience, I only did a rough visual check of a few regions (e.g., frontal and temporal lobes) and haven’t verified each region in detail.

As some colors were repeated in the visualization of all brain regions, I split the regions into four groups of 12 and made separate plots for easier inspection. You can find the region mapping table at the end of this comment.

Could you please check if the region mapping is correct?
Thank you so much in advance!

Group 1: region 01-12

In this group, I noticed clear asymmetry in the coloring of certain regions between the left and right hemispheres. Upon inspection, I found that the labels for the right hemisphere were incorrect. The corrected labeling is shown in the figure below and primarily involves the following regions: 09 Frontal_Sup_Medial, 10 Frontal_Med_Orb, 11 Rectus.

Group 2: region 13-24

Group 3: region 25-36

Group 4: region 37-41

Region Mapping

index	region	aal_id_L	aal_id_R
1	Precentral	2001	2002
2	Frontal_Sup_2	2101	2102
3	Frontal_Mid_2	2201	2202
4	Frontal_Inf_Oper	2301	2302
5	Frontal_Inf_Tri	2311	2312
6	Frontal_Inf_Orb_2	2321	2322
7	Rolandic_Oper	2331	2332
8	Supp_Motor_Area	2401	2402
9	Frontal_Sup_Medial	2601	2602
10	Frontal_Med_Orb	2611	2612
11	Rectus	2701	2702
12	OFCmed	2801	2802
13	OFCant	2811	2812
14	OFCpost	2821	2822
15	OFClat	2831	2832
16	Insula	3001	3002
17	Cingulate_Ant	4001	4002
18	Cingulate_Mid	4011	4012
19	Cingulate_Post	4021	4022
20	ParaHippocampal	4111	4112
21	Amygdala	4201	4202
22	Calcarine	5001	5002
23	Cuneus	5011	5012
24	Lingual	5021	5022
25	Occipital_Sup	5101	5102
26	Occipital_Mid	5201	5202
27	Occipital_Inf	5301	5302
28	Fusiform	5401	5402
29	Postcentral	6001	6002
30	Parietal_Sup	6101	6102
31	Parietal_Inf	6201	6202
32	SupraMarginal	6211	6212
33	Angular	6221	6222
34	Precuneus	6301	6302
35	Paracentral_Lobule	6401	6402
36	Heschl	8101	8102
37	Temporal_Sup	8111	8112
38	Temporal_Pole_Sup	8121	8122
39	Temporal_Mid	8201	8202
40	Temporal_Pole_Mid	8211	8212
41	Temporal_Inf	8301	8302

[FrancisOWO]

Hi,

With the help of participants to this issue, I have updated the region mapping and surface visualization, and carefully inspected all brain regions one by one in the surface image. I believe the region labels are now correct—please see this comment for details.