Dear BST community,
When using the default ICBM152 anatomy, I typically run the CAT12 segmentation on it to get the Schafer atlases. I've done this for a while now, with no issues.
However, I am running into the following error I've never come across before.
Apologizes in advance if this is a CAT12 issue and not a BST one.
Any assistance with this would be greatly appreciated.
Thank you,
Paul
Indeed, in the latest version of CAT (r1904), the function cat_surf_map_atlas.m makes a reference to a variable ST that is not used before, at line 62.
@CGaser
Could you please look into this?
@pdhami
While this gets fixed, you can probably download and use an older version of CAT:
cat_surf_map_atlas.m does not include the same error$HOME/.brainstorm/plugins/cat12/cat12 with the contents of the cat12 folder you've just downloaded$HOME/.brainstorm/plugins/cat12, as a symbolic link redirects $HOME/.brainstorm/plugins/spm12/spm12/toolbox/cat12 to it. If you the folder, you'd need to recreate the link manuallyHi Francois,
I am still running into similar errors, although I don't know if I was able to properly follow the replacement of the CAT12 contents.
I tried custom install through the plug in manager, but got that the version of CAT12 I downloaded was not able to be recognized. Could I do the install through the plug in manager?
I did exactly as you suggested, but reported this error:
** Error: Line 60: Output argument "varargout{2}" (and maybe others) not assigned during call to "cat_system".
**
** Call stack:
** >cat_surf_map_atlas.m at 60
** >process_segment_cat12.m>Compute at 382
** >process_segment_cat12.m>ComputeInteractive at 445
** >process_segment_cat12.m at 28
** >bst_call.m at 28
** >tree_callbacks.m>@(h,ev)bst_call(@process_segment_cat12,'ComputeInteractive',iSubject,iAnatomy) at 3005
**
Do you have any suggestions?
Thank you very much for your help!
I also tried to install the old version of cat on my own, but in the process of running it brainstorm reported that it was not working properly and needed to be reinstalled
BST> =================================
SPM12 template found: /home/jade/.brainstorm/defaults/spm/TPM.nii
BST> Checking latest online version for cat12...
BST> Processing dependencies: cat12 requires: spm12
BST> Plugin cat12 already loaded: /home/jade/app/brainstorm3/cat12
** Error: SPM must be in the Matlab path to use this feature.
BST> Adding plugin spm12 to path: /home/jade/.brainstorm/plugins/spm12/spm12
BST> Executing callback LoadedFcn: spm('defaults','EEG');
SPM12 template found: /home/jade/.brainstorm/defaults/spm/TPM.nii
BST> Processing dependencies: cat12 requires: spm12
BST> Plugin cat12 already loaded: /home/jade/app/brainstorm3/cat12
** Error: Cannot identify CAT12 version: please re-install it.
I guess I shouldn't have sent you on the tracks of trying to install manually an older version of CAT without testing this myself first... Let me try to provide an easier fix for this issue, until it gets fixed in CAT.
edit cat_surf_map_atlas (you need the CAT plugin to be loaded for this function to be available in the path)% at the beginning of the line (comment only the if/end lines, and keep the entire block in between, as we want the new parcellations to be saved)Thank you Francois! All seems to be working now.
@CGaser just pushed a fix to this problem.
You can now update to CAT12 version 1906 and it should fix the problem.