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Bug 2388 - consider adding support for cytoarchitectonic atlas

Reported 2013-11-22 14:26:00 +0100
Modified 2014-01-15 14:48:27 +0100
Product: FieldTrip
Component: core
Version: unspecified
Hardware: PC
Operating System: Windows
Importance: P3 enhancement
Assigned to: Jan-Mathijs Schoffelen
Depends on:
See also:

Eelke Spaak - 2013-11-22 14:26:51 +0100

E.g. the one available in the SPM Anatomy toolbox: It cannot currently be read in by ft_read_atlas, it seems.

Jan-Mathijs Schoffelen - 2013-11-24 12:43:20 +0100

Did you look into the toolbox? Looks like a mess to me. Before we spend time on implementing support, do you think it really adds to the currently supported atlases, in particular the aal-atlas? A similar question can be asked for support for the PALS B12 atlas. Also when looking into the downloaded atlas the directory structure really brings tears to ones eyes. We should discuss whether it's worthwile to implement this one, particularly, because WashU advertises Conte69 as the one to use (which is supported by ft_read_atlas). See bug 1876 for this

Eelke Spaak - 2013-11-25 09:11:31 +0100

(In reply to comment #1) Yes I looked at the toolbox, though not in great detail. I saw some .img files which I suspected might be compatible with the current ft_read_atlas implementation, but apparently they are not. It adds over the AAL atlas that you get Brodmann area labels, rather than macroanatomical labels. Although there is a 1:1 mapping in most cases, I must admit. Anyway, this is low-priority I think, just thought I'd file it away as a reminder. Maybe mark wontfix?

Jan-Mathijs Schoffelen - 2013-11-25 09:14:19 +0100

I think it should be relatively straightforward, but I was put off initially by the fact that there's a subdirectory that seems to contain probabilistic masks (or could be binary) per area. I'd rather just have a single 3D volume that labels the areas with plain indices.

Jan-Mathijs Schoffelen - 2013-11-25 11:33:59 +0100

support added as of revision 8843.

Jan-Mathijs Schoffelen - 2013-11-25 11:48:51 +0100

updated documentation on wiki template/atlas/

Eelke Spaak - 2013-11-25 12:15:50 +0100

(In reply to comment #4) Merci!