Hi !
I'm installing SPM12. I noticed that pickatlas is not developed for SPM12. Nevertheless, I tried. I did not succeed to install pickatlas with an installation as for SPM8.

I am not waiting for answer, I just send errors to the developpers of pickatlas… but I can test new scripts if you want...
Isabelle


TEST1 on matlab R2014:
   - no pickatlas in the 'toolbox' menu
   - error when taping 'wfu_pickatlas in the matlab window :
>> wfu_pickatlas
Error using fileparts
Too many output arguments.
Error in wfu_require_spm_lite (line 59)
[tbxCommonPath f e j] = fileparts(mfilename('fullpath'));
Error in wfu_pickatlas (line 21)
wfu_require_spm_lite({'SPM5','SPM8', 'SPM12'});

The fourth output argument of fileparts (file version) is no longer supported and has been removed. Calling the function with more than three output arguments generates an error.


TEST2 on matlab 7.6 (R2008a) :
   - pickatlas is in the 'toolbox' menu, works (at least I did not use it: just open some human templates)
but then it was impossible to quit spm and matlab :
??? Error using ==> wfu_spm at 169
Unknown action string ('Quit'). It possible that
F:\spm12\toolbox\wfu_tbx_common\spm_lite is incorrectory listed in your
path and should be removed.

Error in ==> spm at 9
wfu_spm(varargin{:});

   - tapping 'wfu_pickatlas' in the matlab window : OK

Hi Isabelle,
  Thanks for finding that bug (re TEST1).  Attached is an updated version.  Using the PickAtlas from the command line should be possible in SPM12.  Using it within SPM12 to do ROI analysis is not currently available.  Watch for an update to do that.

  For TEST2 I would expect that the PickAtlas was added to the path with a genpath command.  This shouldn't be done.  Only add the wfu_pickatlas directory (and maybe the wfu_tbx_common).

Please let me know if there are further questions, comments, or concerns,

Best,
Ben

TEST1 with matlab 8.3:
OK. thank you !

TEST2 with matlab 7.6 :
set path with genpath (may be it would by easier to change the command in the manual…):
addpath(genpath('F:\spm12\toolbox\wfu_pickatlas'));

then the paths include the following :
F:\spm12\toolbox\wfu_results
F:\spm12\toolbox\wfu_tbx_common\spm_lite
F:\spm12\matlabbatch\cfg_basicio
F:\spm12\toolbox\deface
F:\spm12\toolbox\Shoot
F:\spm12\toolbox\OldSeg
F:\spm12\toolbox\OldNorm
F:\spm12\toolbox\Longitudinal
F:\spm12\toolbox\FieldMap
F:\spm12\toolbox\DARTEL
F:\spm12\config
F:\spm12\matlabbatch
F:\spm12\toolbox\wfu_pickatlas
F:\spm12\toolbox\wfu_pickatlas\MNI_atlas_templates
F:\spm12\toolbox\wfu_pickatlas\MNI_atlas_templates\legacy
F:\spm12\toolbox\wfu_pickatlas\MNI_atlas_templates\legacy\EXTRAS
F:\spm12\toolbox\wfu_pickatlas\MNI_atlas_templates\legacy\EXTRAS\ORIGINAL
F:\spm12\toolbox\wfu_pickatlas\MNI_atlas_templates\legacy\EXTRAS\PCG_Modified
F:\spm12\toolbox\wfu_pickatlas\TD-ICBM_MNI_atlas_templates
F:\spm12\toolbox\wfu_pickatlas\TD-ICBM_MNI_atlas_templates\legacy
F:\spm12\toolbox\wfu_pickatlas\mouse_atlas_templates
F:\spm12\toolbox\wfu_pickatlas\rhesus_atlas_templates
F:\spm12\toolbox\wfu_pickatlas\vervet_atlas_templates

but same error :

??? Error using ==> wfu_spm at 169
Unknown action string ('Quit'). It possible that
F:\spm12\toolbox\wfu_tbx_common\spm_lite is incorrectory listed in your path and should be removed.

Error in ==> spm at 9
wfu_spm(varargin{:});
??? Error while evaluating uicontrol Callback


may be an important information: installation is on a server (windows2003) with 4 versions of SPM installed and many users.
to start SPM, the user choose the SPM version which runs a script: for SPM12 it starts with :
rmpath (genpath('F:\spm2'));
rmpath (genpath('F:\spm5'));
rmpath (genpath('F:\spm8'));
rmpath (genpath('F:\snpm5b'));
addpath(genpath('F:\spm12'));
addpath(genpath('F:\spm12\toolbox\wfu_pickatlas')); 
addpath(genpath('F:\SnPM13')); 
spm

I think that adding the path for pick-atlas is not useful (same result with or without).

Hi Isabelle,
  I was not clear.  One should NOT add pickatlas (and SPM) paths with genpath.  The lines:

addpath(genpath('F:\spm12'));
addpath(genpath('F:\spm12\toolbox\wfu_pickatlas'));

actually add all the pickatlas stuff twice.  The more correct way would be:

addpath('F:\spm12');
addpath('F:\spm12\toolbox\wfu_pickatlas');
addpath('Other toolboxes that might need to be added to path');

Again, with SPM 12 all you'll be able to do is define ROIs.  I don't know if the results viewer works with 12.  ROI analysis through the "RESULTS" button won't work either.

Hope this helps,
Ben

Thank you Benjamin.
Sorry to have misunderstood...
I changed the path as you said. The paths after opening the toolbox inside SPM12 are :

F:\spm12\toolbox\wfu_results
F:\spm12\toolbox\wfu_tbx_common\spm_lite
F:\spm12\toolbox\wfu_tbx_common
F:\spm12\matlabbatch\cfg_basicio
F:\spm12\toolbox\deface
F:\spm12\toolbox\Shoot
F:\spm12\toolbox\OldSeg
F:\spm12\toolbox\OldNorm
F:\spm12\toolbox\Longitudinal
F:\spm12\toolbox\FieldMap
F:\spm12\toolbox\DARTEL
F:\spm12\config
F:\spm12\matlabbatch
F:\SnPM13
F:\spm12\toolbox\wfu_pickatlas
F:\spm12
….

but impossible to close spm :
??? Error using ==> wfu_spm at 169
Unknown action string ('Quit'). It possible that F:\spm12\toolbox\wfu_tbx_common\spm_lite is incorrectory listed in
your path and should be removed.

Error in ==> spm at 9
wfu_spm(varargin{:});
??? Error while evaluating uicontrol Callback

---------

when opening spm12 (before opening wfu_pickatlas), paths are :
F:\spm12\matlabbatch\cfg_basicio
F:\spm12\toolbox\deface
F:\spm12\toolbox\Shoot
F:\spm12\toolbox\OldSeg
F:\spm12\toolbox\OldNorm
F:\spm12\toolbox\Longitudinal
F:\spm12\toolbox\FieldMap
F:\spm12\toolbox\DARTEL
F:\spm12\config
F:\spm12\matlabbatch
F:\SnPM13
F:\spm12\toolbox\wfu_pickatlas
F:\spm12
...

----
I tested the same thing with matlab8.3 and I can't close spm :

Error using fileparts
Too many output arguments.

Error in wfu_spm (line 168)
[l_path file ext junk] = fileparts(x);
Error in spm (line 9)
wfu_spm(varargin{:});
Error while evaluating uicontrol Callback

Ok, so the scripts are working as they should...adding in the spm_lite because it is not recognizing SPM12.  This is to be expected (sort of) and will be fixed when we release it for SPM12.

Thanks for bringing this to my attention.
Ben

> thank you and good luck !