I'm trying to use the GRETNA toolbox to process some rs-fMRI data. But it is choking on the delete images step. I've used the default of 10 images and did not change any other settings. The MATLAB errors that I get are:

Undefined function 'fieldnames' for input arguments of type 'double'.

Error in psom_pipeline_init (line 305)
list_jobs = fieldnames(pipeline);

Error in psom_run_pipeline (line 379)
[tmp,flag_start] = psom_pipeline_init(pipeline,opt_init);

  Error in gretna_GUI_PreprocessInterface>RunEvent (line 2311)
psom_run_pipeline(pipeline,opt);

  Error in gretna_GUI_PreprocessInterface>RunButton_Callback (line 2431)
RunEvent(hObject , handles);

  Error in gui_mainfcn (line 96)
  feval(varargin{:});

  Error in gretna_GUI_PreprocessInterface (line 42)
  gui_mainfcn(gui_State, varargin{:});
 
Error in 
@(hObject,eventdata)gretna_GUI_PreprocessInterface('RunButton_Callback',hObject,eventdata,guidata(hObject))
 
  Error while evaluating uicontrol Callback

Any Ideas?

Hi Bryson,
If you use 3D NifTi Data, GRETNA will not really execute "Delete Images"
step to images and just select the images which you want for following steps.
So if you use only this step, GRETNA wouldn't create a pipeline, then failed.

You can try to add another step together to test it.

Hope it will be helpful to you.

Best,
Sandy

Yes, I am using 3D NifTi files, but it did work for some of my subjects. So, I stopped trying the delete images step, and it's now choking on the slice timing correction (usually fails on the 2nd or 3rd participant). I've verified the number of slices, slice acquisition order, and am using the last slice as the reference slice. I'll admit I'm still relatively new to SPM'd preprocessing but it seems that I have everything in order. Any ideas why this might be failing?

Hi Bryson,
I suppose you have the latest version SPM8, if not, update SPM 8 first.
Then check your data manually to ensure your raw data is fine:)
Finally you can try to process the failed data with SPM interface to
get the error message and send to me.

If it is still not work, you can send GRETNA log file to me.
It is at GretnaLogs, I will try to find what happened.

Best
Sandy

The slice timing is inconsistent, i got the file to work when I ran it by itself. Now the problem I am having is with the normalization. Some of the files are getting normalized poorly. I believe that it has to do with the bounding box. Do you have any suggestions about how to choose a robust bounding box or do I need to have a unique bounding box for each participant?

Now I'm running with a file on which normalization ran well. It's currently failing on Detrend, now the error that I'm getting is:

Something went bad ... the job has FAILED !
The last error message occured was :
Error using mat2file
Subscripted assignment dimension mismatch (2).
File /Users/bryson/Documents/MATLAB/spm8/@file_array/subsasgn.m at line 132
File /Users/bryson/Documents/MATLAB/spm8/@file_array/subsasgn.m at line 70
File /Users/bryson/Documents/MATLAB/spm8/spm_write_plane.m at line 33
File /Users/bryson/Documents/MATLAB/GRETNA/GUI/gretna_detrend.m at line 42
File /Users/bryson/Documents/MATLAB/psom-1.0.2/psom_run_job.m at line 214
File /Users/bryson/Documents/MATLAB/psom-1.0.2/psom_run_job.m at line 128

Any ideas?

Hi Bryson,
Sorry for the late,
It seems that SPM cannot write the result matrix to file,
I guess it is still a problem that some version's SPM8 was
incompatible to GRETNA.
You can try to test spm_write_plane function to ensure it can accept
cell-style input for the first one, if not, try to update to the newest
version SPM8 which I use, too.
If it is still not work, we can try to find any other problem to make it
run.

Best,
Sandy

I am up-to-date with SPM8 unless it's changed in the last 2 weeks. I'm leaning toward doing the preprocessing directly in SPM8 and then maybe feeding it back into GRETNA.

I am also trying to use the GRETNA Toolbox to do the voxel-based degree. The Matlab errors that I have are:

Error using gretna_GUI_PreprocessInterface>RefreshStatus (line 2563)

Error in gretna_GUI_PreprocessInterface>RunEvent (line 2513)
RefreshStatus(handles.AliasList, handles.InputListbox, handles.PipelineLog);
Error in gretna_GUI_PreprocessInterface>RunButton_Callback (line 2640)
RunEvent(hObject , handles);
Error in gui_mainfcn (line 96)
feval(varargin{:});
Error in gretna_GUI_PreprocessInterface (line 42)
gui_mainfcn(gui_State, varargin{:});
Error in @(hObject,eventdata)gretna_GUI_PreprocessInterface('RunButton_Callback',hObject,eventdata,guidata(hObject))
Error while evaluating uicontrol Callback
Undefined function 'CalInterface' for input arguments of type 'char'.
Error in gretna_GUI_PreprocessInterface>PopupMenu_Callback (line 2744)
CalInterface('Connect');
Error in gui_mainfcn (line 96)
feval(varargin{:});
Error in gretna_GUI_PreprocessInterface (line 42)
gui_mainfcn(gui_State, varargin{:});
Error in @(hObject,eventdata)gretna_GUI_PreprocessInterface('PopupMenu_Callback',hObject,eventdata,guidata(hObject))
Error while evaluating uicontrol Callback

I tried to run this toolbox on Matlab 2015 and Matlab 2013, and I got the same errors.
Any help would be highly appreciated.

Gaelle

Hi Gaelle,
GRETNA call psom to run pipeline in background,
The error message in command line was just errors
about read logfile, please click "Refresh" button on
GUI and chekc the status of pipeline.

If it was failed, ensure your BrainMask had the same
resolution with your data.

If you have any other questions, just leave a
message.

Best,
Sandy

Hi Gaelle,

I have the same problem as you. Has your problem been solved? How is it solved?

Hello everyone!

I'm trying to use GRETNA toolbox to generate Functional Connectivity Matrix of fMRI images (in DICOM format). I am using Macbook Pro(2017) 2.9 GHz Dual-Core Intel Core i5, macOS Catilina.
After configuring all the Preprocessing steps, when i hit RUN, Matlab gives the following error:

Log of the (matlab) job : T1Dcm2Nii00001
Started on 29-Mar-2020 23:54:33
User: ishanjain
host : Ishans-MacBook-Pro-3.local
system : unix
******************************
The job starts now !
********************
zsh:1: bad CPU type in executable: ./dcm2nii_mac
********************
Something went bad ... the job has FAILED !
The last error message occured was :
Error using gretna_RUN_T1Dcm2Nii (line 42)
Error when DICOM to NIfTI
File /Users/ishanjain/Desktop/softwares/GRETNA/RunFun/gretna_RUN_T1Dcm2Nii.m at line 42
File /Users/ishanjain/Desktop/softwares/GRETNA/PSOM/psom_run_job.m at line 214
File /Users/ishanjain/Desktop/softwares/GRETNA/PSOM/psom_run_job.m at line 128

regarding conversion of Dicom to Nifty. I think the executable file Dcm2Nii_mac can't be run by the OS.
Is is related to 32-bit/64-bit fat binaries

Any sort of help is appreciate .
Thanks

Hi Ishan,

The problem may be due to running macOS Catalina. I'm not sure that some of
the neuroimaging tools, such as dcm2nii, have support beyond Sierra or High
Sierra. If your machine can run another OS, I would try running this on
Sierra. If you can use a Docker container to run some of the steps that are
not Catalina-compatible and then run the MATLAB portion after that
pre-processing, you may be able to get by without installing a different OS
or licensing MATLAB on a virtual machine.

Cheers,
Paul

I use dcm2niix regularly on Catalina with no problem.  I just tested dcm2nii to see if it runs - it does.  I didn't check it's output though.

Blaise

HI, I am having issues with the Gretna GUI where once I press the group Id naming button or to specify the threshold sequence it gives me the following errors.

Error using inputdlg (line 67)
This function only accepts strings as its first parameter.

Error in gretna_GUI_NetAnalysisInterface>ChangedAction (line 1541)
Ans=inputdlg({'Input Current Item'}, 'Current Item',...
Error in gretna_GUI_NetAnalysisInterface>OptItemList_Callback (line 428)
ChangedAction(hObject);
Error in gui_mainfcn (line 95)
feval(varargin{:});
Error in gretna_GUI_NetAnalysisInterface (line 42)
gui_mainfcn(gui_State, varargin{:});
Error in
matlab.graphics.internal.figfile.FigFile/read>@(hObject,eventdata)gretna_GUI_NetAnalysisInterface('OptItemList_Callback',hObject,eventdata,guidata(hObject))
Error while evaluating UIControl Callback.

Help will be greatly appreciated.

Kind Regards,
Sumit

Hi Sumit,

I have the same issues as you when press the group Id naming button or to specify the threshold sequence, and I would like to know if your problem was solved and how it was solved.

Looking forward to your reply

Kind regards

Madonna

My problem is not solved