Showing 1-11 of 11 posts
Display:
Results per page:
Sep 20, 2014  09:09 AM | Bryson Reynolds - University of Virginia
GRETNA
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?
Sep 22, 2014  12:09 AM | Xin-di Wang
GRETNA
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
Sep 24, 2014  06:09 AM | Bryson Reynolds - University of Virginia
RE: GRETNA
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?
Sep 24, 2014  08:09 AM | Xin-di Wang
RE: GRETNA
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
Sep 24, 2014  03:09 PM | Bryson Reynolds - University of Virginia
RE: GRETNA
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?
Sep 25, 2014  08:09 AM | Bryson Reynolds - University of Virginia
RE: GRETNA
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?
Sep 25, 2014  09:09 AM | Xin-di Wang
RE: GRETNA
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
Sep 25, 2014  02:09 PM | Bryson Reynolds - University of Virginia
RE: GRETNA
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.
May 5, 2016  01:05 PM | Gaelle Doucet
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
May 5, 2016  09:05 PM | Xin-di Wang
GRETNA
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
Dec 27, 2018  08:12 AM | Fu Changyang
RE: GRETNA
Hi Gaelle,

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