open-discussion > Problem with WFU Pick Atlas
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Oct 9, 2014 11:10 AM | Frank Oltmanns
Problem with WFU Pick Atlas
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
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
Oct 10, 2014 04:10 PM | Xenophon Papademetris
Problem with WFU
Pick Atlas
Where is WFUATLASDIR right now, what is the path?
Xenios
Xenios
Oct 13, 2014 09:10 AM | Frank Oltmanns
RE: Problem with WFU Pick Atlas
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 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
Oct 14, 2014 06:10 PM | Xenophon Papademetris
RE: Problem with
WFU Pick Atlas
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
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
Oct 15, 2014 01:10 PM | Frank Oltmanns
RE: Problem with WFU Pick Atlas
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
Thank you Xenios, your last post was very useful.
Frank