Hi gPPi experts,

I tried gPPI with tutorial data with SPM12 (v6470, 03-Jun-2015). It has no problem when running through all tutorial scripts. However, when I update SPM12 to recent version (v6906, 20-Oct-2016) and run the same tutorial scripts. The gPPi halted when estimated gPPI design. Here is the error message:

SPM12: spm_spm (v6842) 16:09:54 - 29/11/2016
========================================================================

SPM12: spm_est_non_sphericity (v6827) 16:09:55 - 29/11/2016
========================================================================
Estimation Failed
Warning: Missing conditions!!! Invalid Contrast
Invalid Contrast
PPI Contrasts were not estimated for some reason.

--------

When I try spm_spm(SPM) with gPPI SPM.mat. It goes smoothly without error. It seems that it is not the problem from SPM12's estimation.

The SPM12 v6906 change the version number of spm_spm from v6015 to v6842, and change spm_est_non_sphericity from v6015 to v6827. I guess the updated spm_spm or spm_est_non_sphericity cannot pass variables to PPPI. Does anyone know how to solve this problem?

Many thanks,
Yu-Shiang

Dear All,

I believe this modified version of spm_estimate_PPI.m will solve the issue. If the new m-file does not solve the issue, please let me know.

Future of the gPPI Toolbox:
The long-term goal is to build gPPI as a standalone tool that can integrate with fsfast, spm, and/or fmristat for the estimation step. The base code will likely be in R. This should make the toolbox easier to maintain across platforms and software and eliminate the requirement of matlab.

There may also be certain advantages of moving in this direction, such as being able to add histories to nifti files and working with minc files.

Overall, this means the the core code will be separate from the estimation and contrast AND a script will be provided based on the estimation tool that the user wants to use. The base code will be validated against the full SPM implementation before release.

Best,
Donald

Thank you so much for the effort on this great toolbox!

I just installed the new spm_estimate_PPI.m and spm_spm_WB.m in recent post and give it a try again.
However, this time gPPI stoped at spm_fMRI_dsign. Here is the error message:

SPM12: spm_fMRI_design (v5183) 14:51:29 - 02/12/2016
========================================================================
Saving fMRI design : ...SPM.mat saved
estimate_PPI.m
Estimation Failed
Warning: Missing conditions!!! Invalid Contrast
Invalid Contrast
PPI Contrasts were not estimated for some reason.

-----

Sorry I don't have any clue how this happen. If I can help on clarifying something, please let me know.

Many thanks,
Yu-Shiang Su

Hi all,
I think it's due to a bug in the spm_est_non_sphericity with the latest release of SPM12 (please search ''Errors with SPM modelestimate'' in spm email list). Please copy the spm_est_non_sphericity.m file to your SPM installation and it will solve this problem (with the original version of spm_estimate_PPI.m).
Best,
Feng Zhou

 
Originally posted by Feng Zhou:
I tried but failed. The error is 
SPM12: spm_spm (v6842) 15:08:08 - 09/04/2018
========================================================================

SPM12: spm_est_non_sphericity (v6827) 15:08:08 - 09/04/2018
========================================================================
Estimation Failed
Warning: Missing conditions!!! Invalid Contrast
Invalid Contrast
Warning: Missing conditions!!! Invalid Contrast
Invalid Contrast
Warning: Missing conditions!!! Invalid Contrast
Invalid Contrast
PPI Contrasts were not estimated for some reason.

I wonder if PPPI could run with SPM12.

The file spm_est_non_sphericity.m you mentioned is not accessable on the Internet. Would you mind my asking if you could nicely upload the matlab file?

Thanks

Jiahua Xu

My Environment SPM12 v6827 PPPIv 13.1

Hello all and @Donald McLaren,

What is the best way to run a gPPI to estimate task connectivity at the moment?

I was thinking to try the CONN toolbox, but I read your post here about the future of the gPPI toolbox and what was planned.

Is this toolbox at the moment working? Is it indeed working on a stand-alone version which can do the job reliably?


Please share any info and valuable advise on that?

Thank you a lot in advance!,

Best,
Pan.

It should be working. Can you provide the error message that you are getting?
Originally posted by Panagiotis Iliopoulos:

Dear Donald,

I am trying to run the sample data to check for proper installation of the gPPI toolbox. I get the following output and then errors:

P =

struct with fields:
subject: 'sampleData_Study'
directory: '/mnt/resource/f.linsen/gPPI/running_gPPI_generic/sampleData/stats'
VOI: '/mnt/resource/f.linsen/gPPI/running_gPPI_generic/rmedPrecCing.nii'
Region: 'rmedPrec'
analysis: 'psy'
method: 'cond'
Estimate: 1
contrast: 0
extract: 'eig'
Tasks: {1×13 cell}
Weights: []
equalroi: 1
FLmask: 0
CompContrasts: 1
Contrasts: [1×2 struct]
Log File: sampleData_Study_PPPI_6_9_2022_2.log
PPPI Version: 13.1.4-17-2014
Parameters used:
Processing subject: sampleData_Study
VOI file : /mnt/resource/f.linsen/gPPI/running_gPPI_generic/rmedPrecCing.nii
Output file will be: sampleData_Study_rmedPrec_session#_cond_PPI_regressors.txt
Contrast : No adjustment
Analysis : Psychophysiological Interactions
Extraction : eigenvariate
Tasks : _0_etoh_on_onsets_run1_etoh_off_onsets_run1_etoh_urge_onsets_run1_attn_on_onsets_run1_attn_off_onsets_run1_attn_urge_onsets_run1_etoh_on_onsets_run2_etoh_off_onsets_run2_etoh_urge_onsets_run2_attn_on_onsets_run2_attn_off_onsets_run2_attn_urge_onsets_run2
Method : Condition Specific
VOI has 549 voxels in 3x3x3 space
VOI has 549 voxels in 3x3x3 space. This is in the the same space as the input data and functional mask.

Operands to the || and && operators must be convertible to logical scalar
values.
Error in dlmwrite (line 133)
useVectorized = realdata && precnIsNumeric && ~contains('%\',dlm) ...
Error in PPPI (line 861)
dlmwrite([P.subject '_' region1 '_session' num2str(z) '_' P.method
'_PPI_regressors.txt'],[OUT.PPI.C OUT.P.C OUT.Y.C OUT.C.C],' ');
Error in runOnSampleData (line 49)
PPPI(P, ['/mnt/resource/f.linsen/gPPI/running_gPPI_generic' filesep
'sampleData' filesep 'stats' filesep 'gPPI_sampleDataTest.mat']);


Hope to hear from you!

Kind regards,
Ploon

sorry, managed to fix it myself. Worked by renaming the contains.m file; this answer was already given on this forum!

Hello, 

I am having the same error as you did:

Error in runOnSampleData (line 49)
PPPI(P, ['/Users/marinefleury/Desktop/gPPI/running_gPPI_generic' filesep 'sampleData' filesep 'stats' filesep 'gPPI_sampleDataTest.mat']

How did you fix your error please? I tried renaming the contains.m file in the PPPIv13 folder but it is still not working.

I would be very grateful if you could help me with this.

Thank you!
Kind regards,
Marine