error in Population module

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Timothy Ellmore

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Sep 15, 2020, 3:33:05 PM9/15/20

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Hello,

I've been using ExploreASL v1.2.0 for the past month. Congrats on making a much needed comprehensive ASL analysis package.

I am analyzing a longitudinal study of 20 patients scanned twice (T1, FLAIR, and ASL 6 months apart). Things work well in all modules until I reach the Population module, when I receive the error listed below. Does anyone know what's wrong or how I can debug this?

Many thanks,

Tim

====================================================================================

Running xASL_module_Population ...

++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

Starting xASL_module_Population at 15-Sep-2020 02:09:19

Searching T1 images:100%, loading images:100%

Computing T1_n=40 parametric map(s)...

ERROR: Job iteration terminated!

ans =

'Unrecognized function or variable 'Sets2Check'.

Error in xASL_wrp_CreatePopulationTemplates (line 323)

elseif isempty(Sets2Check)

Error in xASL_module_Population (line 74)

xASL_wrp_CreatePopulationTemplates(x); % this doesn't work nicely yet with sessions, should be changed after new BIDS is implemented

Error in xASL_Iteration>runIteration (line 361)

[result, x] = jobfn(x); % [result, x] = jobfn(x, job_ex);

Error in xASL_Iteration (line 100)

[bAborted, xOut] = runIteration(dbSettings);

Error in ExploreASL_Master (line 143)

[~, x] = xASL_Iteration(x,'xASL_module_Population');

Error in ExploreASL (line 33)

x = ExploreASL_Master(var1, var2, var3, var4, var5, var6);'

CONT: but continue with next iteration!

Job-iteration 1 stopped at 15-Sep-2020 02:09:39 and took 20 seconds

++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++100%

xASL_module_Population completed

Many thanks for using ExploreASL, please don't forget to cite https://pubmed.ncbi.nlm.nih.gov/32526385/

Note that ExploreASL is a collaborative effort.

Therefore, please don't hesitate to contribute by feedback, adding code snippets, or clinical experience!

ans =

struct with fields:

name: 'MSCP1'

subject_regexp: '^\d{2}(|_\d*)$'

M0: 'UseControlAsM0'

M0PositionInASL4D: [1 2]

readout_dim: '2D'

Quality: 1

DELETETEMP: 1

Vendor: 'Philips'

Q: [1×1 struct]

LabelingType: 'CASL'

Initial_PLD: 1800

LabelingDuration: 1800

Sequence: '2D_EPI'

M0_GMScaleFactor: 10

nWorkers: 1

iWorker: 1

S: [1×1 struct]

ProcessData: 1

MyPath: '/Applications/ExploreASL-ExploreASL-495ecc6'

D: [1×1 struct]

stopaftererrors: Inf

dryrun: 0

bOverwrite: 1

Version: '1.2.0'

SpaghettiDir: '/Volumes/Drobo1/ASL/MSCP1/analysis/Population/SpaghettiPlots'

HistogramDir: '/Volumes/Drobo1/ASL/MSCP1/analysis/Population/Histograms'

StatsMaps: '/Volumes/Drobo1/ASL/MSCP1/analysis/Population/StatsMaps'

SPMDIR: '/Applications/ExploreASL-ExploreASL-495ecc6/External/SPMmodified'

SPMpath: '/Applications/ExploreASL-ExploreASL-495ecc6/External/SPMmodified'

SPMVERSION: 'SPM12'

skull: [121×145×121 logical]

BILAT_FILTER: 0

WBmask: [121×145×121 logical]

bReproTesting: 0

Pediatric_Template: 0

bLesionFilling: 1

bAutoACPC: 1

SegmentSPM12: 0

M0_conventionalProcessing: 0

bGetControlLabelOrder: 1

TotalSubjects: {40×1 cell}

nTotalSubjects: 40

exclusion: {''}

SESSIONS: {'ASL_1'}

nSessions: 1

TimePointTotalSubjects: {{1×20 cell} {1×20 cell}}

ExcludedSubjects: ''

SUBJECTS: {1×40 cell}

TotalInclusionList: [40×1 double]

nSubjects: 40

nExcluded: 0

nSubjectsSessions: 40

nTimePointsTotal: 2

nTimePointTotalSubjects: [20 20]

TimePointSubjects: {{1×20 cell} {1×20 cell}}

nTimePoints: 2

nTimePointSubjects: [20 20]

TimePointExcluded: {'' ''}

nTimePointExcluded: [0 0]

P: [1×1 struct]

RERUN: 0

MUTEXID: 'xASL_module_Population'

LockDir: '/Volumes/Drobo1/ASL/MSCP1/analysis/lock/xASL_module_Population'

SUBJECTDIR: '/Volumes/Drobo1/ASL/MSCP1/analysis/20_2'

ModuleName: 'ASL'

result: 1

mutex: [1×1 xASL_GoNoGo]

iSubject: 40

DoWADQCDC: 0

WMHsegmAlg: 'LPA'

SkipIfNoFlair: 0

SkipIfNoASL: 0

SkipIfNoM0: 0

bFixResolution: 0

Seg: [1×1 struct]

T1BiasFieldRegularization: 1

SESSIONDIR: '/Volumes/Drobo1/ASL/MSCP1/analysis/20_2/ASL_1'

SUBJECT: '20_2'

SESSION: 'ASL_1'

ApplyQuantification: [1 1 1 1 1]

iSession: 1

iSubjectSession: 40

SavePWI4D: 0

motion_correction: 1

Modality: 'MR'

MagneticFieldStrength: 3

ImagingFrequency: 127.7700

ManufacturersModelName: 'Ingenia'

InstitutionName: 'UT_Health_Science_Center'

InstitutionalDepartmentName: 'MRI'

InstitutionAddress: '6431_Fannin_Street_Houston_TX_77030'

DeviceSerialNumber: '71191'

StationName: 'INTERA'

BodyPartExamined: 'HEAD'

PatientPosition: 'HFS'

ProcedureStepDescription: 'MRI_BRAIN_WO_CONTRAST'

SoftwareVersions: '5.4.1_5.4.1.1'

SeriesDescription: 'SOURCE_-_pCASL'

ProtocolName: 'WIP_SOURCE_-_pCASL'

ScanningSequence: 'GR'

SequenceVariant: 'SK'

ScanOptions: 'FS'

ImageType: {6×1 cell}

SeriesNumber: 1102

AcquisitionTime: '123234.63'

AcquisitionNumber: 11

PhilipsRWVIntercept: 0

UsePhilipsFloatNotDisplayScaling: 0

SliceThickness: 5

SpacingBetweenSlices: 6

SAR: 0.3067

EchoTime: 15.8270

RepetitionTime: 4550

FlipAngle: 90

CoilString: 'MULTI_COIL'

PartialFourier: 0.4432

PercentPhaseFOV: 100

EchoTrainLength: 39

PhaseEncodingSteps: 88

AcquisitionMatrixPE: 88

ReconMatrixPE: 128

PixelBandwidth: 2047

PhaseEncodingAxis: 'j'

ImageOrientationPatientDICOM: [6×1 double]

InPlanePhaseEncodingDirectionDICOM: 'COL'

ConversionSoftware: 'dcm2niix'

ConversionSoftwareVersion: 'v1.0.20181125 Clang8.1.0'

RWVSlope: 1.3756

RescaleSlope: 1.3756

RescaleIntercept: 0

MRScaleSlope: 0.0154

ResolutionEstimation: 0

PathPop_MaskSusceptibility: '/Volumes/Drobo1/ASL/MSCP1/analysis/Population/rMaskSusceptibility_20_2_ASL_1.nii'

DUMMY: ''

Henk-Jan Mutsaerts

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Sep 16, 2020, 3:19:46 AM9/16/20

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Dear Tim,

Yes, we found this bug and fixed it in our release from this week (r1.2.1), see https://github.com/ExploreASL/ExploreASL/issues/102.

Longitudinal ASL analyses have not been performed a lot, if you want we can discuss further how to properly address this including longitudinal confounds.

We also have a weekly user meeting on Friday afternoon that you are welcome to join!

Best, Henk

Henk(-Jan) Mutsaerts, MD PhD

Amsterdam UMC/ UZ Ghent/UCL/Mutsaerts Research

Phone: +31 6 4390 8284; Skype: hj.mutsaerts

Jan Petr

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Sep 16, 2020, 3:23:03 AM9/16/20

to ExploreASL

Dear Tim,

Thanks for reporting this. We have fixed this error in version 1.2.1, which has just been released.

You can download it here https://github.com/ExploreASL/ExploreASL/archive/master.zip

Or through other channels (github.com/ExploreASL/ExploreASL or exploreasl.org or https://zenodo.org/record/4030411#.X2G85uHniXI).

Let us know if this wouldn't fix your issue (note that you *might* need to remove some of the Population module lock files prior to re-run).

best regards,

Jan

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