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help > RE: Potential bugs in preprocessing pipeline
Sep 5, 2018 06:09 AM | Pravesh Parekh - National Institute of Mental Health and Neurosciences
RE: Potential bugs in preprocessing pipeline
Dear Dr. Alfonso,
Thank you for the patch. The first time I ran parallel processing by skipping slice timing correction, I got the following error:
Then I tried to run the indirect pipeline and I got the error that the function conn_get_rt is undefined.
I removed Conn from my MATLAB path, restarted MATLAB, and then added Conn back to path. However, now the preprocessing GUI won't load. Below is the error:
and the error on the command prompt:
What could be going wrong?
Thanks and Regards
Pravesh
Originally posted by Alfonso Nieto-Castanon:
Thank you for the patch. The first time I ran parallel processing by skipping slice timing correction, I got the following error:
ERROR DESCRIPTION:
Index exceeds matrix dimensions.Error in conn_setup_preproc (line 636)respatialdef={};Error in conn (line 918)ok=conn_setup_preproc('',varargin{2:end});Error in conn_menumanager (line 120)feval(CONN_MM.MENU{n0}.callback{n1}{1},CONN_MM.MENU{n0}.callback{n1}{2:end});CONN v.18.aSPM12 + DEM FieldMap MEEGtools cat12Matlab v.2016astorage: 14307.8Gb availablespm @ /usr/local/MATLAB/R2016a/toolbox/spm12conn @ /usr/local/MATLAB/R2016a/toolbox/conn
SUGGESTIONS:
Potential missing Setup information. Try revising Setup fields for potential missing information
Index exceeds matrix dimensions.Error in conn_setup_preproc (line 636)respatialdef={};Error in conn (line 918)ok=conn_setup_preproc('',varargin{2:end});Error in conn_menumanager (line 120)feval(CONN_MM.MENU{n0}.callback{n1}{1},CONN_MM.MENU{n0}.callback{n1}{2:end});CONN v.18.aSPM12 + DEM FieldMap MEEGtools cat12Matlab v.2016astorage: 14307.8Gb availablespm @ /usr/local/MATLAB/R2016a/toolbox/spm12conn @ /usr/local/MATLAB/R2016a/toolbox/conn
SUGGESTIONS:
Potential missing Setup information. Try revising Setup fields for potential missing information
Then I tried to run the indirect pipeline and I got the error that the function conn_get_rt is undefined.
I removed Conn from my MATLAB path, restarted MATLAB, and then added Conn back to path. However, now the preprocessing GUI won't load. Below is the error:
ERROR DESCRIPTION:
Reference to non-existent field 'label'.
Error in conn_setup_preproc>@(n)sprintf('Process secondary dataset #%d %s',n,regexprep(CONN_x.Setup.secondarydataset(n).label,'(.+)','($1)')) (line 402)
if any(cellfun('length',regexp(dlg.steps_names,'^functional'))), dlg.m10=uicontrol('style','popupmenu','units','norm','position',[.05,.13,.3,.05],'value',1+sets,'string',[{'Process primary dataset'},arrayfun(@(n)sprintf('Process secondary dataset #%d %s',n,regexprep(CONN_x.Setup.secondarydataset(n).label,'(.+)','($1)')),1:numel(CONN_x.Setup.secondarydataset),'uni',0)],'tooltipstring','Apply this preprocessing to selected dataset in your curent CONN project (the same dataset will hold the output files)
- note: only when preprocessing the primary dataset (dataset-0) non-essential preprocessing outputs (ROIs, first- and
second- level covariates) will be automatically imported into your CONN project','visible','on','fontsize',9+font_offset);
Error in conn_setup_preproc (line 402)
if any(cellfun('length',regexp(dlg.steps_names,'^functional'))), dlg.m10=uicontrol('style','popupmenu','units','norm','position',[.05,.13,.3,.05],'value',1+sets,'string',[{'Process primary dataset'},arrayfun(@(n)sprintf('Process secondary dataset #%d %s',n,regexprep(CONN_x.Setup.secondarydataset(n).label,'(.+)','($1)')),1:numel(CONN_x.Setup.secondarydataset),'uni',0)],'tooltipstring','Apply this preprocessing to selected dataset in your curent CONN project (the same dataset will hold the output files)
- note: only when preprocessing the primary dataset (dataset-0) non-essential preprocessing outputs (ROIs, first- and
second- level covariates) will be automatically imported into your CONN project','visible','on','fontsize',9+font_offset);
Error in conn (line 918)
ok=conn_setup_preproc('',varargin{2:end});
Error in conn_menumanager (line 120)
feval(CONN_MM.MENU{n0}.callback{n1}{1},CONN_MM.MENU{n0}.callback{n1}{2:end});
CONN v.18.a
SPM12 + DEM FieldMap MEEGtools cat12
Matlab v.2016a
storage: 14306.9Gb available
spm @ /usr/local/MATLAB/R2016a/toolbox/spm12
conn @ /usr/local/MATLAB/R2016a/toolbox/conn
Reference to non-existent field 'label'.
Error in conn_setup_preproc>@(n)sprintf('Process secondary dataset #%d %s',n,regexprep(CONN_x.Setup.secondarydataset(n).label,'(.+)','($1)')) (line 402)
if any(cellfun('length',regexp(dlg.steps_names,'^functional'))), dlg.m10=uicontrol('style','popupmenu','units','norm','position',[.05,.13,.3,.05],'value',1+sets,'string',[{'Process primary dataset'},arrayfun(@(n)sprintf('Process secondary dataset #%d %s',n,regexprep(CONN_x.Setup.secondarydataset(n).label,'(.+)','($1)')),1:numel(CONN_x.Setup.secondarydataset),'uni',0)],'tooltipstring','Apply this preprocessing to selected dataset in your curent CONN project (the same dataset will hold the output files)
- note: only when preprocessing the primary dataset (dataset-0) non-essential preprocessing outputs (ROIs, first- and
second- level covariates) will be automatically imported into your CONN project','visible','on','fontsize',9+font_offset);
Error in conn_setup_preproc (line 402)
if any(cellfun('length',regexp(dlg.steps_names,'^functional'))), dlg.m10=uicontrol('style','popupmenu','units','norm','position',[.05,.13,.3,.05],'value',1+sets,'string',[{'Process primary dataset'},arrayfun(@(n)sprintf('Process secondary dataset #%d %s',n,regexprep(CONN_x.Setup.secondarydataset(n).label,'(.+)','($1)')),1:numel(CONN_x.Setup.secondarydataset),'uni',0)],'tooltipstring','Apply this preprocessing to selected dataset in your curent CONN project (the same dataset will hold the output files)
- note: only when preprocessing the primary dataset (dataset-0) non-essential preprocessing outputs (ROIs, first- and
second- level covariates) will be automatically imported into your CONN project','visible','on','fontsize',9+font_offset);
Error in conn (line 918)
ok=conn_setup_preproc('',varargin{2:end});
Error in conn_menumanager (line 120)
feval(CONN_MM.MENU{n0}.callback{n1}{1},CONN_MM.MENU{n0}.callback{n1}{2:end});
CONN v.18.a
SPM12 + DEM FieldMap MEEGtools cat12
Matlab v.2016a
storage: 14306.9Gb available
spm @ /usr/local/MATLAB/R2016a/toolbox/spm12
conn @ /usr/local/MATLAB/R2016a/toolbox/conn
and the error on the command prompt:
Struct contents reference from a non-struct
array object.
Error in conn_setup_preproc>conn_setup_preproc_update (line 2887)
val=get(dlg.m0,'value');
Error in conn_setup_preproc>@(varargin)conn_setup_preproc_update (line 389)
dlg.m0=uicontrol('style','popupmenu','units','norm','position',[.05,.85,.85,.05],'string',steps_names(steps_order),'value',find(ismember(steps_order,selectedstep)),'backgroundcolor',1*[1
1 1],'foregroundcolor','k','tooltipstring','Select a data preprocessing
step','callback',@(varargin)conn_setup_preproc_update,'fontsize',9+font_offset);
Error while evaluating UIControl Callback
Error in conn_setup_preproc>conn_setup_preproc_update (line 2887)
val=get(dlg.m0,'value');
Error in conn_setup_preproc>@(varargin)conn_setup_preproc_update (line 389)
dlg.m0=uicontrol('style','popupmenu','units','norm','position',[.05,.85,.85,.05],'string',steps_names(steps_order),'value',find(ismember(steps_order,selectedstep)),'backgroundcolor',1*[1
1 1],'foregroundcolor','k','tooltipstring','Select a data preprocessing
step','callback',@(varargin)conn_setup_preproc_update,'fontsize',9+font_offset);
Error while evaluating UIControl Callback
What could be going wrong?
Thanks and Regards
Pravesh
Originally posted by Alfonso Nieto-Castanon:
Dear
Pravesh,
Thanks for the bug report and perfectly detailed info. I believe the attached patch should fix both of these problems. Could please give it a try and let me know whether you still run into any issues? (this patch is for release 18a, to install it simply copy the attached file to the conn distribution folder overwriting the file with the same name there)
Thanks again
Alfonso
Originally posted by Pravesh Parekh:
Thanks for the bug report and perfectly detailed info. I believe the attached patch should fix both of these problems. Could please give it a try and let me know whether you still run into any issues? (this patch is for release 18a, to install it simply copy the attached file to the conn distribution folder overwriting the file with the same name there)
Thanks again
Alfonso
Originally posted by Pravesh Parekh:
Dear Dr. Alfonso,
Hope you are doing well. I was playing around with the Conn preprocessing modules and have spotted two behaviour which might not be expected:
1. When running the pipeline in parallel on a local machine, if we select skip slice timing correction, the pipeline does not work but throws up the following error (default pipeline):
The pipeline runs fine in parallel if slice timing is specified or when serial processing is selected.
2. When using the indirect normalization pipeline (MNI), the functional files also get normalized to the voxel size of structural images. The GUI prompts to specify the dimensions of structural and functional image for normalization. The default input for structural is 1 while functional is set to 2 (and is grayed out in indirect pipeline). However, the end result is functional files having voxel dimension 1x1x1. They get normalized to 2x2x2 if the structural is set to 2. Possibly somewhere in the batch, the functional voxel size is wrongly specified to match the structural voxel size?
Both the above were tested using Conn 18.a on MATLAB 2016a running on a RedHat machine. Please let me know if you need any more information.
Thanks and Regards
Pravesh
Hope you are doing well. I was playing around with the Conn preprocessing modules and have spotted two behaviour which might not be expected:
1. When running the pipeline in parallel on a local machine, if we select skip slice timing correction, the pipeline does not work but throws up the following error (default pipeline):
ERROR DESCRIPTION:
Index exceeds matrix dimensions.
Error in conn_setup_preproc (line 636)
if isempty(sliceorder)&&~isempty(sliceorder_select), sliceorder=sliceorder_select_options{sliceorder_select}; end
Error in conn (line 918)
ok=conn_setup_preproc('',varargin{2:end});
Error in conn_menumanager (line 120)
feval(CONN_MM.MENU{n0}.callback{n1}{1},CONN_MM.MENU{n0}.callback{n1}{2:end});
CONN v.18.a
SPM12 + DEM FieldMap MEEGtools cat12
Matlab v.2016a
storage: 14397.5Gb available
spm @ /usr/local/MATLAB/R2016a/toolbox/spm12
conn @ /usr/local/MATLAB/R2016a/toolbox/conn
SUGGESTIONS:
Potential missing Setup information. Try revising Setup fields for potential missing information
Index exceeds matrix dimensions.
Error in conn_setup_preproc (line 636)
if isempty(sliceorder)&&~isempty(sliceorder_select), sliceorder=sliceorder_select_options{sliceorder_select}; end
Error in conn (line 918)
ok=conn_setup_preproc('',varargin{2:end});
Error in conn_menumanager (line 120)
feval(CONN_MM.MENU{n0}.callback{n1}{1},CONN_MM.MENU{n0}.callback{n1}{2:end});
CONN v.18.a
SPM12 + DEM FieldMap MEEGtools cat12
Matlab v.2016a
storage: 14397.5Gb available
spm @ /usr/local/MATLAB/R2016a/toolbox/spm12
conn @ /usr/local/MATLAB/R2016a/toolbox/conn
SUGGESTIONS:
Potential missing Setup information. Try revising Setup fields for potential missing information
The pipeline runs fine in parallel if slice timing is specified or when serial processing is selected.
2. When using the indirect normalization pipeline (MNI), the functional files also get normalized to the voxel size of structural images. The GUI prompts to specify the dimensions of structural and functional image for normalization. The default input for structural is 1 while functional is set to 2 (and is grayed out in indirect pipeline). However, the end result is functional files having voxel dimension 1x1x1. They get normalized to 2x2x2 if the structural is set to 2. Possibly somewhere in the batch, the functional voxel size is wrongly specified to match the structural voxel size?
Both the above were tested using Conn 18.a on MATLAB 2016a running on a RedHat machine. Please let me know if you need any more information.
Thanks and Regards
Pravesh
Threaded View
Title | Author | Date |
---|---|---|
Pravesh Parekh | Sep 1, 2018 | |
Pravesh Parekh | Oct 10, 2018 | |
Pravesh Parekh | Oct 4, 2018 | |
Pravesh Parekh | Sep 17, 2018 | |
Alfonso Nieto-Castanon | Sep 25, 2018 | |
Pravesh Parekh | Sep 26, 2018 | |
Alfonso Nieto-Castanon | Oct 10, 2018 | |
Pravesh Parekh | Oct 11, 2018 | |
Alfonso Nieto-Castanon | Oct 12, 2018 | |
Pravesh Parekh | Dec 6, 2018 | |
Alfonso Nieto-Castanon | Dec 9, 2018 | |
Jeff Browndyke | Dec 10, 2018 | |
Pravesh Parekh | Dec 11, 2018 | |
Pravesh Parekh | Sep 25, 2018 | |
Pravesh Parekh | Sep 12, 2018 | |
Alfonso Nieto-Castanon | Sep 3, 2018 | |
Pravesh Parekh | Sep 5, 2018 | |