help > Stock gPPI script missing VOI2 file, where only a single VOI is unecessary
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Jan 10, 2019 02:01 AM | Mark Green
Stock gPPI script missing VOI2 file, where only a single VOI is unecessary
Dear All,
I am running into this error when running a simple gPPI using the standard tutorial script (with tweaked paths) below, can you advise?
I have already tried the line 278 fix, to account for SPM12,5 and installed the spm_estimate_PPI.m patch.
Many thanks,
Mark
>> PPPI('attention_PPPI_MAT.mat')
ERROR 1: Program will exit. VOI2 file does not exist.
ERROR 2: Program will exit. VOI2 file does not a .img, .nii, or .mat file.
One or more inputs are not correct.
ERROR 1:Program will exit. VOI2 file does not exist.
ERROR 2:Program will exit. VOI2 file does not a .img, .nii, or .mat file.
errorvals saved to errorvals.mat
P.subject='Attention_Tutorial';
P.directory='/PATH/GLM/'
P.VOI= '/PATH/VOI_V2_1.mat';
P.Estimate=1;
P.contrast=0;
P.extract='eig';
P.Tasks={'1' 'Stationary' 'No-Attention' 'Attention'};
P.Weights=[];
P.analysis='psy';
P.method='cond';
P.CompContrasts=1;
P.Weighted=0;
P.Contrasts(1).left={'Attention'};
P.Contrasts(1). right={'No-Attention'};
P.Contrasts(1).STAT='T';
P.Contrasts(1).Weighted=0;
P.Contrasts(1).MinEvents=5;
P.Contrasts(1).name='Attention_minus_No-Attention';
P.Contrasts(2).left={'No-Attention'};
P.Contrasts(2).right={'Attention'};
P.Contrasts(2).STAT='T';
P.Contrasts(2).Weighted=0;
P.Contrasts(2).MinEvents=5;
P.Contrasts(2).name='No-Attention_minus_Attention';
P.Contrasts(3).left={'Attention'};
P.Contrasts(3).right={'Stationary'};
P.Contrasts(3).STAT='T';
P.Contrasts(3).Weighted=0;
P.Contrasts(3).MinEvents=5;
P.Contrasts(3).name='Attention_minus_Stationary';
I am running into this error when running a simple gPPI using the standard tutorial script (with tweaked paths) below, can you advise?
I have already tried the line 278 fix, to account for SPM12,5 and installed the spm_estimate_PPI.m patch.
Many thanks,
Mark
>> PPPI('attention_PPPI_MAT.mat')
ERROR 1: Program will exit. VOI2 file does not exist.
ERROR 2: Program will exit. VOI2 file does not a .img, .nii, or .mat file.
One or more inputs are not correct.
ERROR 1:Program will exit. VOI2 file does not exist.
ERROR 2:Program will exit. VOI2 file does not a .img, .nii, or .mat file.
errorvals saved to errorvals.mat
P.subject='Attention_Tutorial';
P.directory='/PATH/GLM/'
P.VOI= '/PATH/VOI_V2_1.mat';
P.Estimate=1;
P.contrast=0;
P.extract='eig';
P.Tasks={'1' 'Stationary' 'No-Attention' 'Attention'};
P.Weights=[];
P.analysis='psy';
P.method='cond';
P.CompContrasts=1;
P.Weighted=0;
P.Contrasts(1).left={'Attention'};
P.Contrasts(1). right={'No-Attention'};
P.Contrasts(1).STAT='T';
P.Contrasts(1).Weighted=0;
P.Contrasts(1).MinEvents=5;
P.Contrasts(1).name='Attention_minus_No-Attention';
P.Contrasts(2).left={'No-Attention'};
P.Contrasts(2).right={'Attention'};
P.Contrasts(2).STAT='T';
P.Contrasts(2).Weighted=0;
P.Contrasts(2).MinEvents=5;
P.Contrasts(2).name='No-Attention_minus_Attention';
P.Contrasts(3).left={'Attention'};
P.Contrasts(3).right={'Stationary'};
P.Contrasts(3).STAT='T';
P.Contrasts(3).Weighted=0;
P.Contrasts(3).MinEvents=5;
P.Contrasts(3).name='Attention_minus_Stationary';
Jan 16, 2019 03:01 PM | Anne Saulin
RE: Stock gPPI script missing VOI2 file, where only a single VOI is unecessary
Dear Mark,
for me it started to work when I got rid of all the lines containing xxxx.Weighted = 0;
That's P.Weighted=0; and the same for the contrasts.
I have no idea why that worked, but it did. Worth a try ;)
Best and good luck,
Anne
for me it started to work when I got rid of all the lines containing xxxx.Weighted = 0;
That's P.Weighted=0; and the same for the contrasts.
I have no idea why that worked, but it did. Worth a try ;)
Best and good luck,
Anne
Jan 20, 2019 05:01 AM | Mark Green
RE: Stock gPPI script missing VOI2 file, where only a single VOI is unecessary
Dear Anne,
That is interesting. I get contrast invalid errors too, but gPPI runs fine. These contrast invalid errors that I see pertain to the localiser to adjust by rather than the gPPI contrasts themselves. The localiser that I am using is the 'Omnibus F-test for PPI Analyses' rather than the P.weighted=0 declared above (which specifies that the eigenvariate is to be extracted without using a localiser).
My issue pertaining to the VOI2 error file was resolved when I removed a member variable struct VOI2 {} from the parameters.mat. I am not sure where this empty cell array came from. It is consistent with a VOI2 (of the kind required for physiophysiological interaction or psychophysiophysiological interaction) being specified but no file being supplied. I will try to comment in relation to your error on your thread.
Many thanks,
Mark
Log File: Attention_Tutorial_PPPI_1_20_2019.log
PPPI Version: 13.1.4-17-2014
Parameters used:
Processing subject: Attention_Tutorial
VOI file : /-----/GLM/VOI_V2_1.mat
Output file will be: Attention_Tutorial_VOI_V2_1_gPPI_Attention_session#_cond_PPI_regressors.txt
Valid Contrast
Warning: Missing conditions!!! Invalid Contrast
Invalid Contrast
Warning: Missing conditions!!! Invalid Contrast
Invalid Contrast
Valid Contrast
Warning: Missing conditions!!! Invalid Contrast
Invalid Contrast
Warning: Missing conditions!!! Invalid Contrast
Invalid Contrast
Valid Contrast
Warning: Missing conditions!!! Invalid Contrast
Invalid Contrast
Warning: Missing conditions!!! Invalid Contrast
Invalid Contrast
ESS image 4 : ...written ess_0004.nii
spm{F} image 4 : ...written spmF_0004.nii
Saving SPM.mat : ...SPM.mat saved
Contrast : Omnibus F-test for PPI Analyses
Analysis : Psychophysiological Interactions
Extraction : eigenvariate
Tasks : _1_Stationary_No-Attention_Attention
Method : Condition Specific
VOI has 26 voxels in 3x3x3 space
VOI has 26 voxels in 3x3x3 space. This is in the the same space as the input data and functional mask.
That is interesting. I get contrast invalid errors too, but gPPI runs fine. These contrast invalid errors that I see pertain to the localiser to adjust by rather than the gPPI contrasts themselves. The localiser that I am using is the 'Omnibus F-test for PPI Analyses' rather than the P.weighted=0 declared above (which specifies that the eigenvariate is to be extracted without using a localiser).
My issue pertaining to the VOI2 error file was resolved when I removed a member variable struct VOI2 {} from the parameters.mat. I am not sure where this empty cell array came from. It is consistent with a VOI2 (of the kind required for physiophysiological interaction or psychophysiophysiological interaction) being specified but no file being supplied. I will try to comment in relation to your error on your thread.
Many thanks,
Mark
Log File: Attention_Tutorial_PPPI_1_20_2019.log
PPPI Version: 13.1.4-17-2014
Parameters used:
Processing subject: Attention_Tutorial
VOI file : /-----/GLM/VOI_V2_1.mat
Output file will be: Attention_Tutorial_VOI_V2_1_gPPI_Attention_session#_cond_PPI_regressors.txt
Valid Contrast
Warning: Missing conditions!!! Invalid Contrast
Invalid Contrast
Warning: Missing conditions!!! Invalid Contrast
Invalid Contrast
Valid Contrast
Warning: Missing conditions!!! Invalid Contrast
Invalid Contrast
Warning: Missing conditions!!! Invalid Contrast
Invalid Contrast
Valid Contrast
Warning: Missing conditions!!! Invalid Contrast
Invalid Contrast
Warning: Missing conditions!!! Invalid Contrast
Invalid Contrast
ESS image 4 : ...written ess_0004.nii
spm{F} image 4 : ...written spmF_0004.nii
Saving SPM.mat : ...SPM.mat saved
Contrast : Omnibus F-test for PPI Analyses
Analysis : Psychophysiological Interactions
Extraction : eigenvariate
Tasks : _1_Stationary_No-Attention_Attention
Method : Condition Specific
VOI has 26 voxels in 3x3x3 space
VOI has 26 voxels in 3x3x3 space. This is in the the same space as the input data and functional mask.
Jan 21, 2019 10:01 PM | Donald McLaren
RE: Stock gPPI script missing VOI2 file,where only a single VOI is unecessary
>
The P.VOI2={} came from PPPI_checkstruct.m. This should be an empty
variable. In PPPIinputsvalid, this should skip over the error messages that
you were seeing. I'm not sure why it registered as not empty.
The errors pertain to the localiser and are expected. This tests for the
full expansion of derivative terms in the model.
-Donald
The P.VOI2={} came from PPPI_checkstruct.m. This should be an empty
variable. In PPPIinputsvalid, this should skip over the error messages that
you were seeing. I'm not sure why it registered as not empty.
The errors pertain to the localiser and are expected. This tests for the
full expansion of derivative terms in the model.
-Donald