Hello,

I copied the wfu-pickatlas dir (the one containing the MNI_atlas_templates dir) in every suggested standard place but everytime I get the same error message that the atlas could not be found.

I don't know whether setting the value of WFUATLASDIR will solve the problem because I have no idea how to do this.

MAC OSX 10.8.5 / BioImage Suite 3.2b1 / WFU Pickatlas 3.0.4

Thanks in advance

Frank

Where is WFUATLASDIR right now, what is the path?

Xenios

I have placed the Atlas dir in every of the places indicated by the error message.

First I tried /Applications/wfu_pickatlas, then /Applications/bioimagesuite3_base/wfu_pickatlas and then in /usr/local/wfu_pickatlas.
Nothing worked so far.

With wfu_pickatlas I mean the dir containing for instance atlas_type.txt, dilate_cube.m and several other files as well as dirs like MNI_atlas_templates, mouse_atlas_templates and so on.

At the moment this dir resides in /Applications/bioimagesuite3_base/

Hope that info is sufficient.

Frank

First of all if placed in /usr/local/wfu_pickatlas it should be found, so I wonder if you are using a version that is too new for what BioImage Suite was coded to look for. (If need be I can zip the one we have).

BioImage Suite looks for a folder MNI_atlas_templates which should be inside /usr/local/wfu_pickatlas

If it finds that then it looks for files such as TD_lobe.hdr inside that. We have not tested with recent versions so the filenames may have changed.

Xenios

Solved. The latest version of the WFU Pick Atlas uses *.nii instead of *.hdr/*.img. So going back to the previous version (ie 2.5) solved the problem.

Thank you Xenios, your last post was very useful.

Frank