Dear AFNI experts,
I am interested in analyzing nucleus basalis of meynert, but could not find any previous paper using AFNI to analyze it. Is there any way to analyze nucleus basalis of meynert using AFNI?
Thank you,
That tiny region in the basal forebrain is not included in any of the atlases distributed with AFNI or one that we have already created, as far as I can tell. So you have a couple choices. Try to find it or try to make it yourself. The newer version of the Eickhoff-Zilles atlases may have it listed as Ch4 (Cholinergic 4), but I haven’t been able to locate it yet. If you would like to try, then you can use some of these papers as a guide for drawing this yourself. It’s a small region, so it won’t take too long, but it may be difficult to identify on an MRI image.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4366544/
https://www.biorxiv.org/content/biorxiv/early/2017/10/30/211086.full.pdf
https://www.sciencedirect.com/science/article/pii/S1053811908006903
Hi Daniel,
Thank you so much for the response. I just have downloaded SPM’s anatomical toolbox and tried to overlay Nucleus Basalis on MNI152 (attached files). I am not sure if this represents the accurate location of Nucleus Basalis as SPM uses different MNI template?
I read this paper (Stereotaxic probabilistic maps of the magnocellular cell groups in human basal forebrain - PMC) examining probabilistic maps of the basal forebrain. It looks pretty much overwhelming to me so I am not sure I can create this by myself.
Thanks,
Jun
The SPM Anatomy toolbox atlases are in a different space than the standard MNI, one that we call MNI_ANAT. You can shift these over with
@ShiftVolume -MNI_Anat_to_MNI -dset dsetname -prefix newdsetprefix
Daniel,
Thanks again for your help. I am sorry that @Shift_Volume is a little bit confusing to me.
First, dset should be the Nucleus Basalis mask from the SPM anatomy toolbox? I tried it the below command line but keeps showing error.
[hlhp-105:/Data/PMaps] titus% @Shift_Volume -MNI_Anat_to_MNI -dset Bforebrain_4.nii -prefix MBN_mask
opref MBN_mask
++ 3dcopy: AFNI version=AFNI_18.2.15 (Aug 28 2018) [64-bit]
++ 3drefit: AFNI version=AFNI_18.2.15 (Aug 28 2018) [64-bit]
++ Authored by: RW Cox
** ERROR: Can’t open dataset MBN_mask
++ 3drefit processed 0 datasets
++ 3drefit: AFNI version=AFNI_18.2.15 (Aug 28 2018) [64-bit]
++ Authored by: RW Cox
** ERROR: Can’t open dataset MBN_mask
++ 3drefit processed 0 datasets
Second, using the @Shift_Volume command line, I can shift the mask from the SPM anatomy toolbox to AFNI’s MNI space?
Thanks,
Jun
Sorry, that script doesn’t handle NIFTI datasets properly as input with the -prefix option. You can still use it but just a little differently for now.
3dcopy Bforebrain_4.nii MBN_mask.nii
@Shift_Volume -MNI_Anat_to_MNI -dset MBM_mask.nii -no_cp
Daniel,
Thanks again for your help. The command line worked well. Is it converted into AFNI’s MNI space? Screenshots of the overlay on MNI_152 are attached.
Thank you,
Jun
First, I am not a neuroanatomist, so I can’t really say with much confidence whether this is right. It looks roughly right based on the image here: https://www.sciencedirect.com/science/article/pii/S0149763413002066?via%3Dihub#fig0005
Hi Jun and Daniel-
Just chiming in a little to say that to my own eyes your first set of screenshots looked like the mask was more in the internal globus pallidus and after the shift looks better but still more like the central nucleus of the amygdala… so I’d be careful about the initial input masks. I checked FSLeyes and they don’t seem to have the structure, and yes, it’s in SPM’s Anatomy toolbox but I’m not sure what happened during your particular transfer/transform. Manually drawing on the group average of your nonlinearly-normalized structurals shouldn’t be too time-consuming in AFNI, so you may just want to do that. Naturally, only after your eyes have adjusted more to where the structure actually is based on quality work like Zaborszky’s and others.
Just my $0.02, motivated in part by empathy to difficulties dealing with small and under-studied subcortical structures. Good luck!
-Sam