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)
>>>
>>> ===========================================================================
>>>
>>>
>>
>
