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In general, when I am running multiple subjects/seed regions, I execute the commands inside a try statement. This way if a subject fails, it will go on to the next subject. There is no need to reprocess completed subjects.

Using a try statement should avoid the program failing, but might not stop it from hanging.

If you want to track the completed subjects, I'd create a variable and store the subject/region in it after the subject/region is finished processing. Save this once you've appended the next completed subject/region. This would provide a list of which subjects have finished if the program continues to fail/hang.

Is there a consistent person that the script fails or hangs while processing? You could run PPPI on just that subject and get more information about why that subject is problematic.

Best Regards, Donald McLaren
=================
D.G. McLaren, Ph.D.
Research Fellow, Department of Neurology, Massachusetts General Hospital and
Harvard Medical School
Postdoctoral Research Fellow, GRECC, Bedford VA
Website: http://www.martinos.org/~mclaren
Office: (773) 406-2464
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On Tue, Mar 25, 2014 at 11:11 AM, Prerona Mukherjee <[log in to unmask]> wrote:
Hi

thank you so much for your help. the patch definitely helped to fix my problem and everything is running now.

I have one more question. If the program fails or hangs in the middle of the PPI step (PPPI_v_2) after having processed multiple subjects, is there a good way to recover from the point it last got (last subject completely analysed) or do we have to start again from scratch?

Any advice you could give would be great as I have a lot of subjects in my analysis

Sincerely

Prerona







------------------------------------------------------------------------------------------------------------
Prerona Mukherjee

Post Doctoral Research Associate
Stonybrook University
Department of Psychiatry
Putnam Building, Room 135

Work:   631 632-8639
Mobile: 773 916 7662


On Thu, Mar 20, 2014 at 11:47 AM, Luis Morís <[log in to unmask]> wrote:
Hi,

One possible option is that your dataset is too large. A patch was released sometime ago that solves this problem ( http://www.nitrc.org/projects/gppi ) Otherwise I would check task names, any extra space, wrong character,...

If the contrast is not an error but a warning and appears before the estimation they are probably related to the omnibus f-test, and that should be fine (this appears in the manual in the common issues, check if it's your case).

Cheers,

Luis.




On Thu, Mar 20, 2014 at 3:29 PM, Prerona Mukherjee <[log in to unmask]> wrote:

Hi Everyone

I am trying to run the gPPI toolbox and I am getting two errors that I cannot understand. Can anyone give me any advice on this?

I get a message saying "Estimation Failed". When I debug it, it seems to go through the first part of the estimation okay () but at module PPPI, line 784, reference to 'SPM1.VM.fname' fails as there is no VM in the SPM1 structure.


Contrasts step is also giving error.

I have attached my wrapper functions and can send any other error messages or screenshots if someone has any clue / needs more information

===========================================================================
SCREENSHOTS
===========================================================================

In spm_XYZreg (line 383)
[d,i] = min(spm_XYZreg('Edist',varargin{2},varargin{3}));

In create_mask_image (line 61)
    [xyz,i] = spm_XYZreg('NearestXYZ',mask.XYZmm(:,v),XYZmm);

In set_mask (line 94)
         xY.mask=create_mask_image(SPM,region1,xY.XYZmm,maskdir);

In timeseries_extract (line 191)
            [xY,errorchk]=set_mask(SPM,P.VOI,region1,P.maskdir);

In PPPI (line 395)
    timeseries_extract;

In PPPI_v_2 (line 180)
    PPPI(gPPI_struct);

In PPI_script2b2_18_mar (line 99)
    PPPI_v_2(seed,directories,contrasts,prefix,data_dir,rootDIR)
===========================================================================