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help > Hippocampus vs. Amygdala (No. of voxels)
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May 20, 2016 02:05 PM | Pravesh Parekh - National Institute of Mental Health and Neurosciences
Hippocampus vs. Amygdala (No. of voxels)
Greetings!
I am using WFUPickAtlas 3.0.5 (Update 2015-02-12). I have SPM 12 (ver 6470) installed on MATLAB 2015a.
On launching the WFU GUI, I select "Human Atlas". Then I go to "TD Brodmann Areas+" and select "Hippocampus" (3D, Advanced view). I save the ROI as a .nii file. The same process is repeated using "Amygdala" [again using Brodmann Areas]. Do note that left and right ROIs are saved as separate files.
Next, I read these volumes into my MATLAB space and (because these are binary masks), count the number of voxels that are present (by counting the number of 1's):
On doing the above, I have the following results:
Left Amygdala: 161 voxels
Right Amygdala: 158 voxexls
Left Hippocampus: 139 voxels
Right Hippocampus: 122 voxels
The lesser number of voxels in Hippocampus (compared to Amygdala) seems quite odd.
I also did the following (using the supplied aal_MNI_V4.nii file):
Left Amygdala: 220 voxels
Right Amygdala: 248 voxels
Left Hippocampus: 932 voxels
Right Hippocampus: 946 voxels
Can someone explain why when using the Brodmann set of ROIs, we have smaller size of the Hippocampus (as compared to Amygdala) and the source of large discrepancy between the AAL and Brodmann labels (in case of Hippocampus)?
Many Thanks!
Regards
Pravesh
I am using WFUPickAtlas 3.0.5 (Update 2015-02-12). I have SPM 12 (ver 6470) installed on MATLAB 2015a.
On launching the WFU GUI, I select "Human Atlas". Then I go to "TD Brodmann Areas+" and select "Hippocampus" (3D, Advanced view). I save the ROI as a .nii file. The same process is repeated using "Amygdala" [again using Brodmann Areas]. Do note that left and right ROIs are saved as separate files.
Next, I read these volumes into my MATLAB space and (because these are binary masks), count the number of voxels that are present (by counting the number of 1's):
volume =
spm_vol(Amygdala/Hippocampus.nii);
[data xyz] = spm_read_vols(volume);
num_voxels = sum(data(:));
[data xyz] = spm_read_vols(volume);
num_voxels = sum(data(:));
On doing the above, I have the following results:
Left Amygdala: 161 voxels
Right Amygdala: 158 voxexls
Left Hippocampus: 139 voxels
Right Hippocampus: 122 voxels
The lesser number of voxels in Hippocampus (compared to Amygdala) seems quite odd.
I also did the following (using the supplied aal_MNI_V4.nii file):
volume = spm_vol('aal_MNI_V4.nii');
[data xyz] = spm_read_vols(volume);
selected_vox = (data(:,:,:) == 37) %37 corresponds to left hippocampus; similarly 38 for right hippocampus, 41 for left amygdala and 42 for right amygdala
num_voxels = sum(selected_vox(:));
On doing the above I get the following output:[data xyz] = spm_read_vols(volume);
selected_vox = (data(:,:,:) == 37) %37 corresponds to left hippocampus; similarly 38 for right hippocampus, 41 for left amygdala and 42 for right amygdala
num_voxels = sum(selected_vox(:));
Left Amygdala: 220 voxels
Right Amygdala: 248 voxels
Left Hippocampus: 932 voxels
Right Hippocampus: 946 voxels
Can someone explain why when using the Brodmann set of ROIs, we have smaller size of the Hippocampus (as compared to Amygdala) and the source of large discrepancy between the AAL and Brodmann labels (in case of Hippocampus)?
Many Thanks!
Regards
Pravesh
May 20, 2016 07:05 PM | Benjamin Wagner - UT Southwestern Medical Center
RE: Hippocampus vs. Amygdala (No. of voxels)
Hello Pravesh,
I wish I had a better answer, but that is just the differences in the Atlases.
Ben
I wish I had a better answer, but that is just the differences in the Atlases.
Ben
May 20, 2016 07:05 PM | Pravesh Parekh - National Institute of Mental Health and Neurosciences
RE: Hippocampus vs. Amygdala (No. of voxels)
Hello,
Thank you for the reply. So the hippocampus being smaller than amaygdala is not a bug, right?
Regards
Pravesh
Originally posted by Benjamin Wagner:
Thank you for the reply. So the hippocampus being smaller than amaygdala is not a bug, right?
Regards
Pravesh
Originally posted by Benjamin Wagner:
Hello Pravesh,
I wish I had a better answer, but that is just the differences in the Atlases.
Ben
I wish I had a better answer, but that is just the differences in the Atlases.
Ben
May 20, 2016 07:05 PM | Benjamin Wagner - UT Southwestern Medical Center
RE: Hippocampus vs. Amygdala (No. of voxels)
Hello again!
No bugs. You may wish to also look at the TD-ICBM atlas. Also remember both are single subject brains. The TD has the confound of going from Tal space to MNI space (thus the reason to also look at TD-ICBM).
Ben
No bugs. You may wish to also look at the TD-ICBM atlas. Also remember both are single subject brains. The TD has the confound of going from Tal space to MNI space (thus the reason to also look at TD-ICBM).
Ben