help > Error during art preprocessing involving masks: "Attempt to grow array along ambiguous dimension."
Showing 1-3 of 3 posts
Apr 26, 2022 05:04 PM | Karl Lerud
Error during art preprocessing involving masks: "Attempt to grow array along ambiguous dimension."
Hi Alfonso et al. I am getting an error while executing a CONN
batch script, during the functional art preprocessing stage, that I
have not seen before. I haven't studied it very closely yet, but I
was hoping something would jump out at you or someone else. I have
made several changes to my pipelines recently, so it is definitely
possible I have misplaced something, but I haven't found anything
yet. It does get through the art preprocessing of several subjects
and sessions before this, and it looks like it is tripping up on
the second session of this subject. Thanks, appreciate any ideas,
and of course I can provide more details if needed. The error and
stack trace is pasted below, best,
Karl
Mapping files for session 1...: ...done
Calculating globals...: 450/450...done
Mapping files for session 2...: ...done
Calculating globals...: Attempt to grow array along ambiguous dimension.
Error in art>art_OpeningFcn (line 409)
Mask(masktemp)=0;
Error in gui_mainfcn (line 220)
feval(gui_State.gui_OpeningFcn, gui_hFigure, [], guidata(gui_hFigure), varargin{:});
Error in art (line 145)
[varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:});
Error in conn_art (line 8)
[varargout{1:nargout}]=art(varargin{:});
Error in conn_setup_preproc (line 2956)
else h=conn_art('sess_file',matlabbatch{n}.art,'visible','off');
Error in conn_process (line 27)
case 'setup_preprocessing', conn_disp(['CONN: RUNNING SETUP.PREPROCESSING STEP']); conn_setup_preproc(varargin{:});
Error in conn_batch (line 1239)
conn_process('setup_preprocessing',steps,'subjects',SUBJECTS,OPTIONS{:});
Error in multielectrodeCONNsetup_randomEffects3 (line 435)
conn_batch(conn_x)
>>
Karl
Mapping files for session 1...: ...done
Calculating globals...: 450/450...done
Mapping files for session 2...: ...done
Calculating globals...: Attempt to grow array along ambiguous dimension.
Error in art>art_OpeningFcn (line 409)
Mask(masktemp)=0;
Error in gui_mainfcn (line 220)
feval(gui_State.gui_OpeningFcn, gui_hFigure, [], guidata(gui_hFigure), varargin{:});
Error in art (line 145)
[varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:});
Error in conn_art (line 8)
[varargout{1:nargout}]=art(varargin{:});
Error in conn_setup_preproc (line 2956)
else h=conn_art('sess_file',matlabbatch{n}.art,'visible','off');
Error in conn_process (line 27)
case 'setup_preprocessing', conn_disp(['CONN: RUNNING SETUP.PREPROCESSING STEP']); conn_setup_preproc(varargin{:});
Error in conn_batch (line 1239)
conn_process('setup_preprocessing',steps,'subjects',SUBJECTS,OPTIONS{:});
Error in multielectrodeCONNsetup_randomEffects3 (line 435)
conn_batch(conn_x)
>>
Apr 27, 2022 11:04 PM | Alfonso Nieto-Castanon - Boston University
RE: Error during art preprocessing involving masks: "Attempt to grow array along ambiguous dimension."
Hi Karl,
Sorry I've never seen that before, I imagine it may indicate some sort of unusual change in the dimensionality of the functional data across different scans within a single session (?), for example if the functional data has been really concatenated into a single session from multiple sessions that may contain different acquisition FOVs...
Hope this helps
Alfonso
Originally posted by Karl Lerud:
Sorry I've never seen that before, I imagine it may indicate some sort of unusual change in the dimensionality of the functional data across different scans within a single session (?), for example if the functional data has been really concatenated into a single session from multiple sessions that may contain different acquisition FOVs...
Hope this helps
Alfonso
Originally posted by Karl Lerud:
Hi Alfonso et al. I am getting an error while
executing a CONN batch script, during the functional art
preprocessing stage, that I have not seen before. I haven't studied
it very closely yet, but I was hoping something would jump out at
you or someone else. I have made several changes to my pipelines
recently, so it is definitely possible I have misplaced something,
but I haven't found anything yet. It does get through the art
preprocessing of several subjects and sessions before this, and it
looks like it is tripping up on the second session of this subject.
Thanks, appreciate any ideas, and of course I can provide more
details if needed. The error and stack trace is pasted below,
best,
Karl
Mapping files for session 1...: ...done
Calculating globals...: 450/450...done
Mapping files for session 2...: ...done
Calculating globals...: Attempt to grow array along ambiguous dimension.
Error in art>art_OpeningFcn (line 409)
Mask(masktemp)=0;
Error in gui_mainfcn (line 220)
feval(gui_State.gui_OpeningFcn, gui_hFigure, [], guidata(gui_hFigure), varargin{:});
Error in art (line 145)
[varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:});
Error in conn_art (line 8)
[varargout{1:nargout}]=art(varargin{:});
Error in conn_setup_preproc (line 2956)
else h=conn_art('sess_file',matlabbatch{n}.art,'visible','off');
Error in conn_process (line 27)
case 'setup_preprocessing', conn_disp(['CONN: RUNNING SETUP.PREPROCESSING STEP']); conn_setup_preproc(varargin{:});
Error in conn_batch (line 1239)
conn_process('setup_preprocessing',steps,'subjects',SUBJECTS,OPTIONS{:});
Error in multielectrodeCONNsetup_randomEffects3 (line 435)
conn_batch(conn_x)
>>
Karl
Mapping files for session 1...: ...done
Calculating globals...: 450/450...done
Mapping files for session 2...: ...done
Calculating globals...: Attempt to grow array along ambiguous dimension.
Error in art>art_OpeningFcn (line 409)
Mask(masktemp)=0;
Error in gui_mainfcn (line 220)
feval(gui_State.gui_OpeningFcn, gui_hFigure, [], guidata(gui_hFigure), varargin{:});
Error in art (line 145)
[varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:});
Error in conn_art (line 8)
[varargout{1:nargout}]=art(varargin{:});
Error in conn_setup_preproc (line 2956)
else h=conn_art('sess_file',matlabbatch{n}.art,'visible','off');
Error in conn_process (line 27)
case 'setup_preprocessing', conn_disp(['CONN: RUNNING SETUP.PREPROCESSING STEP']); conn_setup_preproc(varargin{:});
Error in conn_batch (line 1239)
conn_process('setup_preprocessing',steps,'subjects',SUBJECTS,OPTIONS{:});
Error in multielectrodeCONNsetup_randomEffects3 (line 435)
conn_batch(conn_x)
>>
May 2, 2022 08:05 PM | Karl Lerud
RE: Error during art preprocessing involving masks: "Attempt to grow array along ambiguous dimension."
Hi Alfonso, thanks. I was able to
solve this, but I'm not sure why it worked. Basically, I usually
have a CAT12 segmentation with voxel size of 2 to do SPM
preprocessing with, so the y_ deformation field and all the
functional volumes would have voxel size 2x2x2 mm. But for whatever
reason, I noticed that this particular session had 1.5x1.5x1.5
voxel size for all those images, making the functional images much
bigger in file size of course. I don't remember where that came
from, so I just re-preprocessed with voxel size of 2, and now the
art preprocessing is working. But I am pretty sure I have done art
preprocessing on this session before, so still not totally sure
what was going on. Let me know if that makes sense to you, but
mostly just wanted to put this here in case someone else encounters
this at some point. Best,
Karl
Originally posted by Alfonso Nieto-Castanon:
Karl
Originally posted by Alfonso Nieto-Castanon:
Hi Karl,
Sorry I've never seen that before, I imagine it may indicate some sort of unusual change in the dimensionality of the functional data across different scans within a single session (?), for example if the functional data has been really concatenated into a single session from multiple sessions that may contain different acquisition FOVs...
Hope this helps
Alfonso
Originally posted by Karl Lerud:
Sorry I've never seen that before, I imagine it may indicate some sort of unusual change in the dimensionality of the functional data across different scans within a single session (?), for example if the functional data has been really concatenated into a single session from multiple sessions that may contain different acquisition FOVs...
Hope this helps
Alfonso
Originally posted by Karl Lerud:
Hi Alfonso et al. I am getting an error while
executing a CONN batch script, during the functional art
preprocessing stage, that I have not seen before. I haven't studied
it very closely yet, but I was hoping something would jump out at
you or someone else. I have made several changes to my pipelines
recently, so it is definitely possible I have misplaced something,
but I haven't found anything yet. It does get through the art
preprocessing of several subjects and sessions before this, and it
looks like it is tripping up on the second session of this subject.
Thanks, appreciate any ideas, and of course I can provide more
details if needed. The error and stack trace is pasted below,
best,
Karl
Mapping files for session 1...: ...done
Calculating globals...: 450/450...done
Mapping files for session 2...: ...done
Calculating globals...: Attempt to grow array along ambiguous dimension.
Error in art>art_OpeningFcn (line 409)
Mask(masktemp)=0;
Error in gui_mainfcn (line 220)
feval(gui_State.gui_OpeningFcn, gui_hFigure, [], guidata(gui_hFigure), varargin{:});
Error in art (line 145)
[varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:});
Error in conn_art (line 8)
[varargout{1:nargout}]=art(varargin{:});
Error in conn_setup_preproc (line 2956)
else h=conn_art('sess_file',matlabbatch{n}.art,'visible','off');
Error in conn_process (line 27)
case 'setup_preprocessing', conn_disp(['CONN: RUNNING SETUP.PREPROCESSING STEP']); conn_setup_preproc(varargin{:});
Error in conn_batch (line 1239)
conn_process('setup_preprocessing',steps,'subjects',SUBJECTS,OPTIONS{:});
Error in multielectrodeCONNsetup_randomEffects3 (line 435)
conn_batch(conn_x)
>>
Karl
Mapping files for session 1...: ...done
Calculating globals...: 450/450...done
Mapping files for session 2...: ...done
Calculating globals...: Attempt to grow array along ambiguous dimension.
Error in art>art_OpeningFcn (line 409)
Mask(masktemp)=0;
Error in gui_mainfcn (line 220)
feval(gui_State.gui_OpeningFcn, gui_hFigure, [], guidata(gui_hFigure), varargin{:});
Error in art (line 145)
[varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:});
Error in conn_art (line 8)
[varargout{1:nargout}]=art(varargin{:});
Error in conn_setup_preproc (line 2956)
else h=conn_art('sess_file',matlabbatch{n}.art,'visible','off');
Error in conn_process (line 27)
case 'setup_preprocessing', conn_disp(['CONN: RUNNING SETUP.PREPROCESSING STEP']); conn_setup_preproc(varargin{:});
Error in conn_batch (line 1239)
conn_process('setup_preprocessing',steps,'subjects',SUBJECTS,OPTIONS{:});
Error in multielectrodeCONNsetup_randomEffects3 (line 435)
conn_batch(conn_x)
>>