Dear Eric,
If I remember correctly, the AAL atlas is distributed in a way directly
compatible with spm_atlas.m, which allows you to make queries from the
command line. By default, it uses the Neuromorphometrics atlas that
comes with SPM12.
There are probably many other tools available to do this, others might
suggest their favourite one. Be mindful that, usually, SPM anatomy
toolbox refers to the JuBrain Anatomy Toolbox:
https://www.fz-juelich.de/inm/inm-7/EN/Resources/_doc/SPM%20Anatomy%20Toolbox_node.html
Best regards,
Guillaume.
On 18/11/2019 15:30, Eric Rawls wrote:
> Hi all,
>
> I am trying to use the SPM anatomy toolbox (AAL) to automatically assign
> anatomical labels to extracted MNI coordinates (X,Y,Z) from fMRI.
>
> This toolbox appears to work well, with the drawback that it does not
> appear to have command line functionality but only gui. Does anybody
> know how to use the AAL toolbox to assign probabilistic anatomical
> labels via command line? If not, can somebody recommend an alternate tool?
>
> We are working with large enough databases that the use of a gui is
> unwieldy for our purposes. While I am aware of the "batch" mode in AAL,
> this does not meet our requirements - a command line labeling tool is
> what we need.
>
> Thanks,
> Eric
> --
> Eric Rawls, Ph.D.
> NIMH T32 Postdoctoral Fellow
> Neuroimaging and Addiction Lab
> Department of Psychiatry and Behavioral Sciences
> University of Minnesota Medical School
> [log in to unmask] <mailto:[log in to unmask]>
--
Guillaume Flandin, PhD
Wellcome Centre for Human Neuroimaging
UCL Queen Square Institute of Neurology
London WC1N 3BG
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