Dear Dr. McLaren,



I'm hoping for your help with the following:

I'm running into an error while running the Sample Data (Matlab 2017a, most recent version SPM12, on a new MacBook). I'm getting an error message identical to "struggling to get SampleData to work on various setups" by O Robinson on Jan 24, 2018 who ran into this issue on a Windows and a Linux machine.



I've followed the recommendations in that thread (checked there is only one pathdef, updating the runOnSampleData.m.Template file with the one attached in that thread and rerunning the bash script), but I keep getting the following error message:



spmpath =
'/Users/VanlutR/MATLAB_addons/spm12'
P =
struct with fields:
subject: 'sampleData_Study'
directory: '/Users/VanlutR/Downloads/NITRC-gppi-Downloads/running_gPPI_generic/sampleData/stats'
VOI: '/Users/VanlutR/Downloads/NITRC-gppi-Downloads/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_5_3_2018_3.log
PPPI Version: 13.1.4-17-2014
Parameters used:
Processing subject: sampleData_Study
VOI file : /Users/VanlutR/Downloads/NITRC-gppi-Downloads/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)
Error in runOnSampleData (line 49)
PPPI(P, ['/Users/VanlutR/Downloads/NITRC-gppi-Downloads/running_gPPI_generic' filesep 'sampleData' filesep
'stats' filesep 'gPPI_sampleDataTest.mat']);
Operands to the || and && operators must be convertible to logical scalar values.
Error in rmiml.visibleInToolstrip
Operands to the || and && operators must be convertible to logical scalar values.
Error in rmiml.visibleInToolstrip

Kind regards,

Remko van Lutterveld
Senior Research Scientist
UMass Medical School

I never actually resolved this and was planning to have another go with an older matlab setup at some point within the next few months. If you do find a solution please do post it here!

Hi All,

This is related to conflicting versions of contains.m in the path.

Please remove contains.m from the PPItoolbox directory. This should resolve the issue.

Best,
Donald

Thanks much for your help :)

The sample data check now gets past the first error, but generates a new one about moving the contrasts.

>> runOnSampleData

spmpath =
'/Users/VanlutR/MATLAB_addons/spm12'
P =
struct with fields:
subject: 'sampleData_Study'
directory: '/Users/VanlutR/running_gPPI_generic/sampleData/stats'
VOI: '/Users/VanlutR/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_5_3_2018_8.log
PPPI Version: 13.1.4-17-2014
Parameters used:
Processing subject: sampleData_Study
VOI file : /Users/VanlutR/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
Error using PPPI (line 420)
Checking for zipped files failed
Error in runOnSampleData (line 49)
PPPI(P, ['/Users/VanlutR/running_gPPI_generic' filesep 'sampleData' filesep 'stats' filesep
'gPPI_sampleDataTest.mat']);
>> cd ~/MATLAB_addons/spm12/tool
Error using cd
Cannot CD to /Users/VanlutR/MATLAB_addons/spm12/tool (Name is nonexistent or not a directory).
>> cd ~/MATLAB_addons/spm12/toolbox/running_gPPI_generic/
>> runOnSampleData
spmpath =
'/Users/VanlutR/MATLAB_addons/spm12'
P =
struct with fields:
subject: 'sampleData_Study'
directory: '/Users/VanlutR/MATLAB_addons/spm12/toolbox/running_gPPI_generic/sampleData/stats'
VOI: '/Users/VanlutR/MATLAB_addons/spm12/toolbox/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_5_3_2018_9.log
PPPI Version: 13.1.4-17-2014
Parameters used:
Processing subject: sampleData_Study
VOI file : /Users/VanlutR/MATLAB_addons/spm12/toolbox/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.
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.
Valid Contrast
Valid Contrast
contrast image 9 : ...written con_0009.nii
spm{T} image 9 : ...written spmT_0009.nii
contrast image 10 : ...written con_0010.nii
spm{T} image 10 : ...written spmT_0010.nii
Saving SPM.mat : ...SPM.mat saved
Moving Contrast Images
error moving contrast PPI_PPI_contrast1
error moving contrast PPI_PPI_contrast1
Moving Contrast Images
error moving contrast PPI_PPI_contrast2
error moving contrast PPI_PPI_contrast2

Update to above: The error message above is the same when I run it on Matlab2015b (with contains.m in the PPPI folder).

Completely forgot to update the solution to the problem above.. It's simply updating the spm_contrasts_PPI.m file with the one in another recent thread on this forum.

Hi ,

I still get the same issue even after removing contains.m file from the toolbox.

Log File: HL001_PPPI_7_18_2019_9.log

PPPI Version: 13.1.4-17-2014
Parameters used:
Processing subject: HL001
VOI file : /Volumes/wangLab/AM/fMRI/long/HL001/GLM/maxima_mask/LIFG_opercularis_11_modified.nii
Output file will be: HL001_LIFG_opercularis_11_bin.nii_session#_cond_PPI_regressors.txt
Contrast : No adjustment
Analysis : Psychophysiological Interactions
Extraction : eigenvariate
Tasks : _0_Control_Rhyming_Semantic
Method : Condition Specific

Error using PPPI (line 420)
Checking for zipped files failed

Do u have any solution for the same?