Hi,

can you kindly assist a query for GRETNA. I have 150 DICOM images for rsfmri scans and 1056 DICOM images for T1. Using GRETNA, I obtained this error but am not sure what the problem is:

>> gretna Thank you for using GRETNA (v2.0.0) Please cite: Wang, J., Wang, X., Xia, M., Liao, X., Evans, A., & He, Y. (2015). GRETNA: a graph theoretical network analysis toolbox for imaging connectomics. Frontiers in human neuroscience, 9, 386. ************************************************************* The pipeline description is now being prepared for execution. The following folder will be used to store logs and status : C:\wtcnapps\Test\GretnaLogs\FunPreproAndNetCon\ ************************************************************* Examining the dependencies of the pipeline ...     Removing empty jobs ...     Checking that all jobs are associated with a command ...     Generating dependencies ...        Reorganizing inputs/outputs ... 0.03 sec        Analyzing job inputs/outputs, percentage completed :  5 10 20 25 35 40 50 55 60 70 75 85 90 100- 0.02 sec     Checking if some outputs were not generated twice ...     Checking if the graph of dependencies is acyclic ...     Cleaning up job status ... Setting up the to-do list. The following jobs will be executed ...     RmFstImg00001       (new)     SliTim00001         (new)     Realign00001        (new)     ChkHM00001          (new)     T1Dcm2Nii00001      (new)     T1CoregSegNorm00001 (new)     ChkNorm00001        (new)     Smooth00001         (new)     Detrend00001        (new)     RegressOut00001     (new)     Filter00001         (new)     Scrubbing00001      (new)     StaticFC00001       (new)     DynamicalFC00001    (new) Checking if all the files necessary to complete the pipeline can be found ... Saving the pipeline description in the logs folder ...     Creating output folders ...     Removing old outputs ...     Creating a 'lock' file C:\wtcnapps\Test\GretnaLogs\FunPreproAndNetCon\\PIPE.lock ...     Saving the individual 'jobs' file C:\wtcnapps\Test\GretnaLogs\FunPreproAndNetCon\\PIPE_jobs.mat ...     Saving the pipeline dependencies in C:\wtcnapps\Test\GretnaLogs\FunPreproAndNetCon\\PIPE.mat...     Saving the 'status' file C:\wtcnapps\Test\GretnaLogs\FunPreproAndNetCon\\PIPE_status.mat ...     Saving the 'logs' file C:\wtcnapps\Test\GretnaLogs\FunPreproAndNetCon\\PIPE_logs.mat ...     Saving the 'profile' file C:\wtcnapps\Test\GretnaLogs\FunPreproAndNetCon\\PIPE_profile.mat ...     Cleaning up old tags and logs from the logs folders ... The pipeline has been successfully initialized ! ******************************************* The pipeline PIPE is now being processed. Started on 09-Sep-2022 13:44:01 user: a, host: unknown, system: windows ******************************************* 09-Sep-2022 13:44:01 RmFstImg00001       submitted (1 run / 0 fail / 0 done / 13 left) 09-Sep-2022 13:44:02 T1Dcm2Nii00001      submitted (2 run / 0 fail / 0 done / 12 left) Warning: File not found or permission denied > In psom_pipeline_process>sub_clean_job (line 797)   In psom_pipeline_process (line 482)   In psom_run_pipeline (line 417)   In gretna_GUI_PreprocessInterface>RunBtn_Callback (line 984)   In gui_mainfcn (line 95)   In gretna_GUI_PreprocessInterface (line 42)   In matlab.graphics.internal.figfile.FigFile/read>@(hObject,eventdata)gretna_GUI_PreprocessInterface('RunBtn_Callback',hObject,eventdata,guidata(hObject)) 09-Sep-2022 13:44:12 RmFstImg00001       failed    (1 run / 1 fail / 0 done / 12 left) Warning: File not found or permission denied > In psom_pipeline_process>sub_clean_job (line 797)   In psom_pipeline_process (line 482)   In psom_run_pipeline (line 417)   In gretna_GUI_PreprocessInterface>RunBtn_Callback (line 984)   In gui_mainfcn (line 95)   In gretna_GUI_PreprocessInterface (line 42)   In matlab.graphics.internal.figfile.FigFile/read>@(hObject,eventdata)gretna_GUI_PreprocessInterface('RunBtn_Callback',hObject,eventdata,guidata(hObject)) 09-Sep-2022 13:44:32 T1Dcm2Nii00001      failed    (0 run / 2 fail / 0 done / 12 left) ********************************************* The processing of the pipeline is terminated. See report below for job completion status. 09-Sep-2022 13:44:32 ********************************************* The execution of the following jobs have failed :     RmFstImg00001 ; T1Dcm2Nii00001 ; More infos can be found in the individual log files. Use the following command to display these logs :     psom_pipeline_visu('C:\wtcnapps\Test\GretnaLogs\FunPreproAndNetCon\','log',JOB_NAME) The following jobs have not been processed due to a dependence on a failed job or the interruption of the pipeline manager :     SliTim00001 ; Realign00001 ; ChkHM00001 ; T1CoregSegNorm00001 ; ChkNorm00001 ; Smooth00001 ; Detrend00001 ; RegressOut00001 ; Filter00001 ; Scrubbing00001 ; StaticFC00001 ; DynamicalFC00001 ; All jobs have been processed, but some jobs have failed. You may want to restart the pipeline latter if you managed to fix the problems. Error using gretna_GUI_PreprocessInterface>RunBtn_Callback (line 1004) \nsub_001\nMATLAB is running in headless mode.  Figure windows will not be displayed. To get started, type doc. For product information, visit www.mathworks.com. Warning: psom:default: The following field(s) were ignored in the structure job :  OutputImgFile > In psom_set_defaults (line 101)   In psom_run_job (line 111) ****************************** Log of the (matlab) job : RmFstImg00001 Started on 09-Sep-2022 13:44:11 User: a host : unknown system : windows ****************************** The job starts now ! ******************** Warning: Cannot recognise format. Trying Analyze. > In read_hdr_raw (line 50)   In read_hdr (line 34)   In nifti (line 26)   In gretna_RUN_RmFstImg (line 18)   In psom_run_job>sub_eval (line 214)   In psom_run_job (line 128) Cannot read header extension. ******************** Something went bad ... the job has FAILED ! The last error message occured was : Insufficient number of outputs from right hand side of equal sign to satisfy assignment. File C:\wtcnapps\GRETNA-master\GUI\gretna_FUN_GetOutputStruct.m at line 5 File C:\wtcnapps\GRETNA-master\RunFun\gretna_RUN_RmFstImg.m at line 28 File C:\wtcnapps\GRETNA-master\PSOM\psom_run_job.m at line 214 File C:\wtcnapps\GRETNA-master\PSOM\psom_run_job.m at line 128 **************** Checking outputs **************** The output file or directory C:\wtcnapps\Test\FunRaw\sub_001\nMT03733_582OK1PDI002.1.5.1.1.1.ima has not been generated! ********************************************** 09-Sep-2022 13:44:12 : The job has FAILED Total time used to process the job : 0.34 sec. ********************************************** ans =   logical    1 \nsub_001\nMATLAB is running in headless mode.  Figure windows will not be displayed. To get started, type doc. For product information, visit www.mathworks.com. Warning: psom:default: The following field(s) were ignored in the structure job :  OutputImgFile > In psom_set_defaults (line 101)   In psom_run_job (line 111) ****************************** Log of the (matlab) job : T1Dcm2Nii00001 Started on 09-Sep-2022 13:44:11 User: a host : unknown system : windows ****************************** The job starts now ! ******************** Chris Rorden's dcm2nii :: 1 April 2010 reading preferences file DCM2NII.INI Validating 1056 potential DICOM images. Found 1056 DICOM images. Converting 176/1056  1 MT03733_582OK1PDI002.1.14.1.1.1.ima->20140818_143252MT03733_582OK1PDI002114111t1nwmtflash3dv2d582-OK-1PDI002MT03733s014a1001.nii GZip 20140818_143252MT03733_582OK1PDI002114111t1nwmtflash3dv2d582-OK-1PDI002MT03733s014a1001.nii Converting 352/1056  1 MT03733_582OK1PDI002.1.14.1.2.177.ima->20140818_143252MT03733_582OK1PDI00211412177t1nwmtflash3dv2d582-OK-1PDI002MT03733s014a2001.nii GZip 20140818_143252MT03733_582OK1PDI00211412177t1nwmtflash3dv2d582-OK-1PDI002MT03733s014a2001.nii Converting 528/1056  1 MT03733_582OK1PDI002.1.14.1.3.353.ima->20140818_143252MT03733_582OK1PDI00211413353t1nwmtflash3dv2d582-OK-1PDI002MT03733s014a3001.nii GZip 20140818_143252MT03733_582OK1PDI00211413353t1nwmtflash3dv2d582-OK-1PDI002MT03733s014a3001.nii Converting 704/1056  1 MT03733_582OK1PDI002.1.14.1.4.529.ima->20140818_143252MT03733_582OK1PDI00211414529t1nwmtflash3dv2d582-OK-1PDI002MT03733s014a4001.nii GZip 20140818_143252MT03733_582OK1PDI00211414529t1nwmtflash3dv2d582-OK-1PDI002MT03733s014a4001.nii Converting 880/1056  1 MT03733_582OK1PDI002.1.14.1.5.705.ima->20140818_143252MT03733_582OK1PDI00211415705t1nwmtflash3dv2d582-OK-1PDI002MT03733s014a5001.nii GZip 20140818_143252MT03733_582OK1PDI00211415705t1nwmtflash3dv2d582-OK-1PDI002MT03733s014a5001.nii Converting 1056/1056  1 MT03733_582OK1PDI002.1.14.1.6.881.ima->20140818_143252MT03733_582OK1PDI00211416881t1nwmtflash3dv2d582-OK-1PDI002MT03733s014a6001.nii GZip 20140818_143252MT03733_582OK1PDI00211416881t1nwmtflash3dv2d582-OK-1PDI002MT03733s014a6001.nii Time elapsed 20172ms ******************** Something went bad ... the job has FAILED ! The last error message occured was : Index exceeds the number of array elements (0). File C:\wtcnapps\GRETNA-master\RunFun\gretna_RUN_T1Dcm2Nii.m at line 46 File C:\wtcnapps\GRETNA-master\PSOM\psom_run_job.m at line 214 File C:\wtcnapps\GRETNA-master\PSOM\psom_run_job.m at line 128 **************** Checking outputs **************** The output file or directory C:\wtcnapps\Test\GretnaT1NIfTI\sub_001\T1.nii has not been generated! *********************************************** 09-Sep-2022 13:44:32 : The job has FAILED Total time used to process the job : 20.51 sec. *********************************************** ans =   logical    1 Error in gui_mainfcn (line 95)         feval(varargin{:}); Error in gretna_GUI_PreprocessInterface (line 42)     gui_mainfcn(gui_State, varargin{:}); Error in matlab.graphics.internal.figfile.FigFile/read>@(hObject,eventdata)gretna_GUI_PreprocessInterface('RunBtn_Callback',hObject,eventdata,guidata(hObject)) Error while evaluating UIControl Callback.

can you kindly let me know what might the problem be please?

James