Error by Unrecognized field name "STRUCT" #1232

aso-toshihiko · 2022-11-07T02:59:04Z

aso-toshihiko
Nov 7, 2022

Hi, I ran 5 subjects each having 6 visits and all of them stopped by this error. Any idea?
I attached the log. Is there any way to save the whole log on the screen with images? I couldn't find such a hypertext-style log in the folderes.
Thanks for the programs!
Toshihiko

{Unrecognized field name "STRUCT".

Error in xASL_init_Iteration (line 92)
    dbSettings.x.dir.LockDir = [dbSettings.x.dir.LockDir '_' x.P.STRUCT ];
Error in ExploreASL_Process (line 107)
    [~, x] = xASL_init_Iteration(x,'xASL_module_LongReg');
Error in ExploreASL (line 97)
    x = ExploreASL_Process(x);
}

ERROR: MATLAB error Exit Status: 0x00000001

Log_STARTINGUPMATLABExploreASL.docx

This is what I got:

MDijsselhof · 2022-11-07T10:38:53Z

MDijsselhof
Nov 7, 2022
Maintainer

Dear Toshihiko,

The reason for this error might be the use of the import module when processing in parallel. This is a feature not currently implemented, but will be added in the future. For now it might be best to try the import separately in a single instance, and once finished perform the processing modules in parallel sessions.

Just to confirm our thoughts, are you using Matlab to process the data, or the GUI?

We hope this helps!

Mathijs, on behalf of the ExploreASL Team

10 replies

aso-toshihiko Nov 8, 2022
Author

Now the process gives this error, for every visits of two subjects, without mutex locked error. Below is a log file from one visit.

[�==============================================================================================]�
=== Subject: sub-A07_1, Module: xASL_module_Structural, 02-Nov-2022 19:35:31 ===

Cleaning data to rerun subject sub-A07_1
No SessionID provided, finding session dirs automatically:
nRemoving lock folders:
Restoring backupped _ORI (original) files:
Deleting native space CAT12 temporary folders:
Deleting native space files for module 1:
Deleting native space files for module 2:
Deleting all standard space files for module 1
Deleting all standard space files for module 2

Removing x-struct and QC-file
Clipped maximal intensity from 209657.7031 to 138208.0938
D:\Saito\kaiseki221102\derivatives\ExploreASL\sub-A07_1\FLAIR.nii is co-registered
D:\Saito\kaiseki221102\derivatives\ExploreASL\sub-A07_1\ASL_1\ASL4D.nii is co-registered
D:\Saito\kaiseki221102\derivatives\ExploreASL\sub-A07_1\ASL_1\ASL4D_Source.nii is co-registered
D:\Saito\kaiseki221102\derivatives\ExploreASL\sub-A07_1\ASL_1\M0.nii is co-registered
D:\Saito\kaiseki221102\derivatives\ExploreASL\sub-A07_1\ASL_2\ASL4D.nii is co-registered
D:\Saito\kaiseki221102\derivatives\ExploreASL\sub-A07_1\ASL_2\ASL4D_Source.nii is co-registered
D:\Saito\kaiseki221102\derivatives\ExploreASL\sub-A07_1\ASL_2\M0.nii is co-registered
Automatic alignment with center of mass: to XYZ:160 254 213
D:\Saito\kaiseki221102\derivatives\ExploreASL\sub-A07_1\FLAIR.nii is co-registered
D:\Saito\kaiseki221102\derivatives\ExploreASL\sub-A07_1\ASL_1\ASL4D.nii is co-registered
D:\Saito\kaiseki221102\derivatives\ExploreASL\sub-A07_1\ASL_1\ASL4D_Source.nii is co-registered
D:\Saito\kaiseki221102\derivatives\ExploreASL\sub-A07_1\ASL_1\M0.nii is co-registered
D:\Saito\kaiseki221102\derivatives\ExploreASL\sub-A07_1\ASL_2\ASL4D.nii is co-registered
D:\Saito\kaiseki221102\derivatives\ExploreASL\sub-A07_1\ASL_2\ASL4D_Source.nii is co-registered
D:\Saito\kaiseki221102\derivatives\ExploreASL\sub-A07_1\ASL_2\M0.nii is co-registered

Rigid-body registering T1.nii to T1.nii
Initialising batch system... done.

Running SPM job 'Coregister: Estimate'

SPM12: spm_coreg (v6435) 19:35:43 - 02/11/2022

Smoothing [2 2 2] into [0 0 0] FWHM resolution
Smoothing [2 2 2] into [0 0 0] FWHM resolution for scan 1
Registering scan 1...
,
Completed : 19:36:13 - 02/11/2022
Done 'Coregister: Estimate'
Done

FLAIR.nii detected, processing...
Clipped maximal intensity from 402413.3438 to 358553.5938
Automatic alignment with center of mass: skipping, was too close

Rigid-body registering FLAIR.nii to T1.nii

Running SPM job 'Coregister: Estimate'

SPM12: spm_coreg (v6435) 19:36:20 - 02/11/2022

Smoothing [0.5 0.473 0.473] into [3.87 4.1 4.1] FWHM resolution
Smoothing [0.5 0.473 0.473] into [3.87 4.1 4.1] FWHM resolution for scan 1
Registering scan 1...
,
Completed : 19:37:03 - 02/11/2022
Done 'Coregister: Estimate'
Done

030_FLAIR_BiasfieldCorrection not requested, skipping...

Reslicing FLAIR.nii to T1.nii using 2nd B-spline interpolation

Running SPM job 'Coregister: Reslice'

SPM12: spm_reslice (v7141) 19:37:06 - 02/11/2022

Completed : 19:37:22 - 02/11/2022
Done 'Coregister: Reslice'
Done

WMH segmentation performed using LST LPA

Running SPM job 'LST: Lesion segmentation (LPA)'

This is LST www.statistical-modeling.de/lst.html
Algorithm: Lesion prediction algorithm (LPA)
If anything goes wrong: LST_log_20221102_193723.txt
Number of jobs to process: 1
Coregister to reference images: no

Working on job 1 out of 1 (100%)
Current directory ...ito/kaiseki221102/derivatives/ExploreASL/sub-A07_1
Preprocessing of rFLAIR.nii Gaussian regularization for bias correction:
Uniform segmentation: Working on planes... 243s
Rough segmentation of FLAIR:
52s
Predict lesion probabilities 10s
Clean up 78s
Finished successfully 02-Nov-2022 19:44:21

Done 'LST: Lesion segmentation (LPA)'
Done

Removing segmented WMH from T1w, and fill lesions with values interpolated from neighborhood
Cleaning up WMH_SEGM:

Running SPM job 'Lesion filling'

Run lesion filling. Visit www.statistical-modeling.de/lst.html
for updates and more information.

Number of images to process: 1

Working on image 1 out of 1 (100%)
Finished successfully on 02-Nov-2022 19:44:55

Done 'Lesion filling'
Done

xASL_Move: overwriting D:\Saito\kaiseki221102\derivatives\ExploreASL\sub-A07_1\T1.nii
No Lesion*.nii specified, cost function masking skipped

Running SPM job 'CAT12: Segmentation'
Loading TPM priors

CAT12.7-Beta r1615: 1/1: .\derivatives\ExploreASL\sub-A07_1\T1.n

Initializing CAT pre-processingSANLM denoising (medium): 118s
Initializing CAT pre-processingInternal resampling (0.50x0.47x0.47mm > 1.00x1.00x1.00mm): 2s
APP: Rough bias correction:
Initialize 4s
Estimate background 2s
Initial correction 4s
Refine background 3s
Final correction 4s
Final scaling 8s
28s
Affine registration 9s
Affine registration 7s
SPM preprocessing 1 (estimate 1): 51s
SPM preprocessing 1 (estimate 2): 55s
Initiate CAT12 main settings: DARTEL enabled
SPM preprocessing 2 (write): ��
Write Segmentation Working on planes... Normalise to sum to 1... 12s
Update Segmentation Clean Up 1:
Also clean up the CSF:
Some slice-work: 24s
Update Skull-Stripping 19s
Update probability maps Update probabiliy maps
correct probability maps to 100%
head to WM correction
head to GM correction
remove brain tissues outside the brainmask ...
spm_MRF: MRF iterations:
�� 3s
0s
Global intensity correction: intensity scaling for gradient estimation: 9s
SANLM denoising after intensity normalization (medium): 6s
Fast registration

Optimized Shooting registration with 3.00:0.00:3.00 mm:
Template: "C:\Users\aso\work\ExploreASL-develop\External\SPMmodified\toolbox\cat12\templates_volumes\Template_0_IXI555_MNI152_GS.nii"
1 | 3.00 | 0.0782 0.0000 0.0782
2 | 3.00 | 0.0731 0.0209 0.0940
3 | 3.00 | 0.0720 0.0025 0.0745
4 | 3.00 | 0.0713 0.0021 0.0734
12 | 3.00 | 0.0821 0.0005 0.0827
13 | 3.00 | 0.0715 0.0037 0.0751
14 | 3.00 | 0.0688 0.0046 0.0734
15 | 3.00 | 0.0672 0.0052 0.0724
16 | 3.00 | 0.0662 0.0055 0.0717
Shooting registration with 3.00:0.00:3.00 mm takes: 12s
Prepare output 4s
16s
Local adaptive segmentation (LASstr=0.50):
Prepare maps 3s
Prepare partitions 1s
Prepare segments (LASmod = 1.00) 7s
Estimate local tissue thresholds (WM) 8s
Estimate local tissue thresholds (GM) 12s
Estimate local tissue thresholds (CSF/BG) 2s
Intensity transformation 33s
SANLM denoising after LAS (medium) 13s
13s
ROI segmentation (partitioning):
Atlas -> subject space 5s
Major structures 3s
Ventricle detection 7s
Blood vessel detection 4s
WMH detection (WMHCstr=0.50 > WMHCstr'=0.32) 18s
Manual stroke lesion detection 0s
Closing of deep structures 1s
Side alignment 2s
Final corrections 1s
42s
Blood vessel correction (BVCstr=0.50): 0s
prepare data for segmentation: Amap using initial SPM12 segmentations (MRF filter strength 0.07): 19s
AMAP peaks: [CSF,GM,WM] = [0.43賊0.08,0.69賊0.07,0.94賊0.06]
Clean Up 1:
Also clean up the CSF:
Some slice-work: Final cleanup (gcutstr=0.25):
Level 1 cleanup (ROI estimation) 2s
Level 1 cleanup (brain masking) 1s
Level 2 cleanup (CSF correction) 0s
Level 3 cleanup (CSF/WM PVE) 0s
4s
No Lesion*.nii specified, not saving the segmentation before masking

Cleaning up NaNs in image: 0%

Optimized Shooting registration with 2.50:-0.25:1.50 mm (regstr=0.50):
Template: "C:\Users\aso\work\ExploreASL-develop\External\SPMmodified\toolbox\cat12\templates_volumes\Template_0_IXI555_MNI152_GS.nii"
1 | 2.50 | 0.0780 0.0000 0.0780
2 | 2.50 | 0.0751 0.0011 0.0762
3 | 2.50 | 0.0742 0.0015 0.0756
4 | 2.50 | 0.0735 0.0016 0.0752
16 | 2.25 | 0.0805 0.0032 0.0837
17 | 2.25 | 0.0675 0.0042 0.0717
18 | 2.25 | 0.0647 0.0046 0.0693
30 | 2.00 | 0.0677 0.0095 0.0772
31 | 2.00 | 0.0617 0.0068 0.0685
32 | 2.00 | 0.0602 0.0074 0.0676
Saving GS intermediate step 3 to a file: D:\Saito\kaiseki221102\derivatives\ExploreASL\sub-A07_1\mri\y_T1_3.nii
44 | 1.75 | 0.0607 0.0112 0.0720
45 | 1.75 | 0.0570 0.0089 0.0659
46 | 1.75 | 0.0562 0.0093 0.0654
58 | 1.50 | 0.0591 0.0127 0.0717
59 | 1.50 | 0.0536 0.0112 0.0648
60 | 1.50 | 0.0524 0.0118 0.0643
Shooting registration with 2.50:-0.25:1.50 mm takes: 108s
Prepare output 4s
112s
Jacobian determinant (RMS): 0.166076
Template Matching: 0.157297
Cleaning up NaNs in image: 0%
Write result maps: Saving the subject-DARTEL transformation as NIfTI
133s
ROI estimation:

CAT Preprocessing error for T1:

File "C: 80 - spm_vol_hdr
61 - spm_vol
74 - cat_main_roi
804 - cat_main
842 - cat_run_job
21 - cat_run_newcatch
866 - run_job
451 - cat_run
29 - cfg_run_cm
1692 - local_runcj
959 - cfg_util
470 - fill_run_job
248 - spm_jobman
609 - xASL_wrp_CAT12Segmentation
179 - xASL_wrp_SegmentT1w
379 - xASL_module_Structural
382 - runIteration
125 - xASL_init_Iteration
92 - ExploreASL_Process
97 - ExploreASL

Print 'Graphics' figure to:
D:\Saito\kaiseki221102\derivatives\ExploreASL\sub-A07_1\report\catreport_SPM12.pdf
Remove "D:\Saito\kaiseki221102\derivatives\ExploreASL\sub-A07_1\label\catROI_T1.xml" from dependency list because it does not exist!
One or multiple files do not exist and were removed from the dependency list
and following batches will may not work correctly!

Remove "D:\Saito\kaiseki221102\derivatives\ExploreASL\sub-A07_1\report\catreport_T1.pdf" from dependency list because it does not exist!
One or multiple files do not exist and were removed from the dependency list
and following batches will may not work correctly!

Remove "D:\Saito\kaiseki221102\derivatives\ExploreASL\sub-A07_1\report\catreportj_T1.jpg" from dependency list because it does not exist!
One or multiple files do not exist and were removed from the dependency list
and following batches will may not work correctly!

Done 'CAT12: Segmentation'
Done

Cleaning up NaNs in image: 0%
Cleaning up WMH_SEGM: 0%

SPM deformation utility executed, using Trilinear interpolation
Transforming C:\Users\aso\work\ExploreASL-develop\External\SPMmodified\MapsAdded\brainmask_supratentorial.nii to D:\Saito\kaiseki221102\derivatives\ExploreASL\sub-A07_1\Temp_mask_Ones.nii
Combining transformations:
Inverse segmentation transformation y_T1.nii of sub-A07_1, to space: Ones.nii

Running SPM job 'Deformations'
Done 'Deformations'
Done

SPM deformation utility executed, using 2nd B-spline interpolation
Transforming D:\Saito\kaiseki221102\derivatives\ExploreASL\sub-A07_1\FLAIR.nii to D:\Saito\kaiseki221102\derivatives\ExploreASL\Population\rFLAIR_sub-A07_1.nii
Transforming D:\Saito\kaiseki221102\derivatives\ExploreASL\sub-A07_1\WMH_SEGM.nii to D:\Saito\kaiseki221102\derivatives\ExploreASL\Population\rWMH_SEGM_sub-A07_1.nii
Transforming D:\Saito\kaiseki221102\derivatives\ExploreASL\sub-A07_1\WMH_SEGM_CleanUp.nii to D:\Saito\kaiseki221102\derivatives\ExploreASL\Population\WMH_SEGM_sub-A07_1_CleanUp.nii
Combining transformations:
Segmentation transformation y_T1.nii of sub-A07_1

Running SPM job 'Deformations'
Done 'Deformations'
Done

xASL_Move: overwriting D:\Saito\kaiseki221102\derivatives\ExploreASL\sub-A07_1\WMH_SEGM.nii
Reslice structural images & move to Population folder

SPM deformation utility executed, using 2nd B-spline interpolation
Transforming D:\Saito\kaiseki221102\derivatives\ExploreASL\sub-A07_1\T1.nii to D:\Saito\kaiseki221102\derivatives\ExploreASL\Population\rT1_sub-A07_1.nii
Transforming D:\Saito\kaiseki221102\derivatives\ExploreASL\sub-A07_1\c1T1.nii to D:\Saito\kaiseki221102\derivatives\ExploreASL\Population\rc1T1_sub-A07_1.nii
Transforming D:\Saito\kaiseki221102\derivatives\ExploreASL\sub-A07_1\c2T1.nii to D:\Saito\kaiseki221102\derivatives\ExploreASL\Population\rc2T1_sub-A07_1.nii
Transforming D:\Saito\kaiseki221102\derivatives\ExploreASL\sub-A07_1\c3T1.nii to D:\Saito\kaiseki221102\derivatives\ExploreASL\Population\rc3T1_sub-A07_1.nii
Transforming D:\Saito\kaiseki221102\derivatives\ExploreASL\sub-A07_1\FLAIR.nii to D:\Saito\kaiseki221102\derivatives\ExploreASL\Population\rFLAIR_sub-A07_1.nii
Combining transformations:
Segmentation transformation y_T1.nii of sub-A07_1

Running SPM job 'Deformations'
Done 'Deformations'
Done

SPM deformation utility executed, using Trilinear interpolation
Transforming D:\Saito\kaiseki221102\derivatives\ExploreASL\sub-A07_1\WMH_SEGM.nii to D:\Saito\kaiseki221102\derivatives\ExploreASL\Population\rWMH_SEGM_sub-A07_1.nii
Combining transformations:
Segmentation transformation y_T1.nii of sub-A07_1

Running SPM job 'Deformations'
Done 'Deformations'
Done

Modulating PV images in standard space

Running SPM job 'Deformations'
Done 'Deformations'
Done

GM volume in native/standard space: 714435, 715751. Difference 0.18%
WM volume in native/standard space: 494623, 495401. Difference 0.16%
CSF volume in native/standard space: 417696, 414489. Difference -0.77%
WMH_SEGM volume in native/standard space: 56060, 56315. Difference 0.45%
[�Warning: catVol.S does not contain the subjectmeasures field...]�
[�> In xASL_wrp_GetVolumetrics (line 38)
In xASL_module_Structural (line 470)
In xASL_init_Iteration>runIteration (line 382)
In xASL_init_Iteration (line 125)
In ExploreASL_Process (line 92)
In ExploreASL (line 97)]�

This is LST www.statistical-modeling.de/lst.html
Algorithm: Compute total lesion volume
Number of images to process: 1
Results are written to LST_tlv_0.05_20221102_205448.csv
Progress 0.0%��100%
Finished successfully on 02-Nov-2022 20:54:56

Couldnt load D:\Saito\kaiseki221102\derivatives\ExploreASL\sub-A07_1\x.mat
Computing anatomical QC parameters from the Preprocessed Connectome Project (PCP) QA Protocol

SPM deformation utility executed, using Nearest Neighbor interpolation
Transforming C:\Users\aso\work\ExploreASL-develop\External\SPMmodified\MapsAdded\CentralWM_QC.nii to D:\Saito\kaiseki221102\derivatives\ExploreASL\sub-A07_1\CentralWM_QC.nii
Transforming C:\Users\aso\work\ExploreASL-develop\External\SPMmodified\MapsAdded\LeftRight.nii to D:\Saito\kaiseki221102\derivatives\ExploreASL\sub-A07_1\LeftRight.nii
Combining transformations:

Reslicing T1.nii to y_T1.nii using Nearest Neighbor interpolation

Running SPM job 'Coregister: Reslice'

SPM12: spm_reslice (v7141) 20:54:59 - 02/11/2022

Completed : 20:55:02 - 02/11/2022
Done 'Coregister: Reslice'
Done

Inverse segmentation transformation y_T1.nii of sub-A07_1, to space: T1.nii

Running SPM job 'Deformations'
Done 'Deformations'
Done

Reslicing CentralWM_QC.nii to T1.nii using Nearest Neighbor interpolation

Running SPM job 'Coregister: Reslice'

SPM12: spm_reslice (v7141) 20:55:08 - 02/11/2022

Completed : 20:55:13 - 02/11/2022
Done 'Coregister: Reslice'
Done

xASL_Move: overwriting D:\Saito\kaiseki221102\derivatives\ExploreASL\sub-A07_1\CentralWM_QC.nii

Reslicing LeftRight.nii to T1.nii using Nearest Neighbor interpolation

Running SPM job 'Coregister: Reslice'

SPM12: spm_reslice (v7141) 20:55:13 - 02/11/2022

Completed : 20:55:18 - 02/11/2022
Done 'Coregister: Reslice'
Done

xASL_Move: overwriting D:\Saito\kaiseki221102\derivatives\ExploreASL\sub-A07_1\LeftRight.nii

SPM deformation utility executed, using Nearest Neighbor interpolation
Transforming D:\Saito\kaiseki221102\derivatives\ExploreASL\sub-A07_1\CentralWM_QC.nii to D:\Saito\kaiseki221102\derivatives\ExploreASL\Population\CentralWM_QC_sub-A07_1.nii
Combining transformations:
Segmentation transformation y_T1.nii of sub-A07_1

Running SPM job 'Deformations'
Done 'Deformations'
Done

Reslicing c1T1.nii to FLAIR.nii using Trilinear interpolation

Running SPM job 'Coregister: Reslice'

SPM12: spm_reslice (v7141) 20:56:01 - 02/11/2022

Completed : 20:56:07 - 02/11/2022
Done 'Coregister: Reslice'
Done

Reslicing c2T1.nii to FLAIR.nii using Trilinear interpolation

Running SPM job 'Coregister: Reslice'

SPM12: spm_reslice (v7141) 20:56:08 - 02/11/2022

Completed : 20:56:14 - 02/11/2022
Done 'Coregister: Reslice'
Done

Computing anatomical QC parameters from the Preprocessed Connectome Project (PCP) QA Protocol

Reslicing CentralWM_QC.nii to FLAIR.nii using Nearest Neighbor interpolation

Running SPM job 'Coregister: Reslice'

SPM12: spm_reslice (v7141) 20:56:16 - 02/11/2022

Completed : 20:56:22 - 02/11/2022
Done 'Coregister: Reslice'
Done

xASL_Move: overwriting D:\Saito\kaiseki221102\derivatives\ExploreASL\sub-A07_1\CentralWM_QC.nii

Reslicing LeftRight.nii to FLAIR.nii using Nearest Neighbor interpolation

Running SPM job 'Coregister: Reslice'

SPM12: spm_reslice (v7141) 20:56:22 - 02/11/2022

Completed : 20:56:28 - 02/11/2022
Done 'Coregister: Reslice'
Done

xASL_Move: overwriting D:\Saito\kaiseki221102\derivatives\ExploreASL\sub-A07_1\LeftRight.nii
Saving QC images

SPM deformation utility executed, using 2nd B-spline interpolation
Transforming D:\Saito\kaiseki221102\derivatives\ExploreASL\sub-A07_1\T1_ORI.nii to D:\Saito\kaiseki221102\derivatives\ExploreASL\Population\rT1_ORI_sub-A07_1.nii
Combining transformations:
Segmentation transformation y_T1.nii of sub-A07_1

Running SPM job 'Deformations'
Done 'Deformations'
Done

Summarizing orientation parameters:
into: D:\Saito\kaiseki221102\derivatives\ExploreASL\sub-A07_1\xASL_qc_PrintOrientation_RigidRegT1.tsv
Collecting QC parameters...

ERROR: Structural module terminated for subject 1: sub-A07_1

ans =

'Unrecognized field name "qualityratings".
 
 Error in xASL_qc_CollectQC_Structural (line 83)
         Struct.T1w_IQR_Perc = min(100,max(0,105 - curr.S.qualityratings.IQR*10));
 
 Error in xASL_qc_CollectParameters (line 64)
     x = QCCollectFunction(x, iSubject);
 
 Error in xASL_wrp_VisualQC_Structural (line 111)
 x = xASL_qc_CollectParameters(x, iSubject, 'Structural');
 
 Error in xASL_module_Structural (line 490)
         xASL_wrp_VisualQC_Structural(x);
 
 Error in xASL_init_Iteration>runIteration (line 382)
 				[result, x] = jobfn(x); % [result, x] = jobfn(x, job_ex);
 
 Error in xASL_init_Iteration (line 125)
     [bAborted, xOut] = runIteration(dbSettings);
 
 Error in ExploreASL_Process (line 92)
         [~, x] = xASL_init_Iteration(x,'xASL_module_Structural');
 
 Error in ExploreASL (line 97)
         x = ExploreASL_Process(x);'

CONT: but continue with next iteration!

Job-iteration 1 stopped at 02-Nov-2022 21:01:58 and took 5187 seconds
[�==============================================================================================]�

[�==============================================================================================]�
=== Subject: sub-A07_1, Module: xASL_module_Structural, 08-Nov-2022 13:11:24 ===

Existing WMH_SEGM.nii detected, so using this WMH_SEGM.nii instead of segmenting ourselves
However, if this WMH_SEGM.nii was created in a previous run, consider removing it first!
010_LinearReg_T1w2MNI has already been performed, skipping...
020_LinearReg_FLAIR2T1w has already been performed, skipping...
WMH segmentation already existing, or FLAIR.nii missing, skipping FLAIR biasfield correction
040_LST_Segment_FLAIR_WMH has already been performed, skipping...
050_LST_T1w_LesionFilling_WMH has already been performed, skipping...
060_Segment_T1w has already been performed, skipping...
080_Resample2StandardSpace has already been performed, skipping...
090_GetVolumetrics has already been performed, skipping...
Couldnt load D:\Saito\kaiseki221102\derivatives\ExploreASL\sub-A07_1\x.mat
Computing anatomical QC parameters from the Preprocessed Connectome Project (PCP) QA Protocol

SPM deformation utility executed, using Nearest Neighbor interpolation
Transforming C:\Users\aso\work\ExploreASL-develop\External\SPMmodified\MapsAdded\CentralWM_QC.nii to D:\Saito\kaiseki221102\derivatives\ExploreASL\sub-A07_1\CentralWM_QC.nii
Transforming C:\Users\aso\work\ExploreASL-develop\External\SPMmodified\MapsAdded\LeftRight.nii to D:\Saito\kaiseki221102\derivatives\ExploreASL\sub-A07_1\LeftRight.nii
Combining transformations:

Reslicing T1.nii to y_T1.nii using Nearest Neighbor interpolation

Running SPM job 'Coregister: Reslice'

SPM12: spm_reslice (v7141) 13:11:29 - 08/11/2022

Completed : 13:11:31 - 08/11/2022
Done 'Coregister: Reslice'
Done

Inverse segmentation transformation y_T1.nii of sub-A07_1, to space: T1.nii

Running SPM job 'Deformations'
Done 'Deformations'
Done

Reslicing CentralWM_QC.nii to T1.nii using Nearest Neighbor interpolation

Running SPM job 'Coregister: Reslice'

SPM12: spm_reslice (v7141) 13:11:36 - 08/11/2022

Completed : 13:11:39 - 08/11/2022
Done 'Coregister: Reslice'
Done

xASL_Move: overwriting D:\Saito\kaiseki221102\derivatives\ExploreASL\sub-A07_1\CentralWM_QC.nii

Reslicing LeftRight.nii to T1.nii using Nearest Neighbor interpolation

Running SPM job 'Coregister: Reslice'

SPM12: spm_reslice (v7141) 13:11:40 - 08/11/2022

Completed : 13:11:43 - 08/11/2022
Done 'Coregister: Reslice'
Done

xASL_Move: overwriting D:\Saito\kaiseki221102\derivatives\ExploreASL\sub-A07_1\LeftRight.nii

SPM deformation utility executed, using Nearest Neighbor interpolation
Transforming D:\Saito\kaiseki221102\derivatives\ExploreASL\sub-A07_1\CentralWM_QC.nii to D:\Saito\kaiseki221102\derivatives\ExploreASL\Population\CentralWM_QC_sub-A07_1.nii
Combining transformations:
Segmentation transformation y_T1.nii of sub-A07_1

Running SPM job 'Deformations'
Done 'Deformations'
Done

Reslicing c1T1.nii to FLAIR.nii using Trilinear interpolation

Running SPM job 'Coregister: Reslice'

SPM12: spm_reslice (v7141) 13:12:20 - 08/11/2022

Completed : 13:12:25 - 08/11/2022
Done 'Coregister: Reslice'
Done

Reslicing c2T1.nii to FLAIR.nii using Trilinear interpolation

Running SPM job 'Coregister: Reslice'

SPM12: spm_reslice (v7141) 13:12:26 - 08/11/2022

Completed : 13:12:31 - 08/11/2022
Done 'Coregister: Reslice'
Done

Computing anatomical QC parameters from the Preprocessed Connectome Project (PCP) QA Protocol

Reslicing CentralWM_QC.nii to FLAIR.nii using Nearest Neighbor interpolation

Running SPM job 'Coregister: Reslice'

SPM12: spm_reslice (v7141) 13:12:33 - 08/11/2022

Completed : 13:12:37 - 08/11/2022
Done 'Coregister: Reslice'
Done

xASL_Move: overwriting D:\Saito\kaiseki221102\derivatives\ExploreASL\sub-A07_1\CentralWM_QC.nii

Reslicing LeftRight.nii to FLAIR.nii using Nearest Neighbor interpolation

Running SPM job 'Coregister: Reslice'

SPM12: spm_reslice (v7141) 13:12:37 - 08/11/2022

Completed : 13:12:42 - 08/11/2022
Done 'Coregister: Reslice'
Done

xASL_Move: overwriting D:\Saito\kaiseki221102\derivatives\ExploreASL\sub-A07_1\LeftRight.nii
Saving QC images

SPM deformation utility executed, using 2nd B-spline interpolation
Transforming D:\Saito\kaiseki221102\derivatives\ExploreASL\sub-A07_1\T1_ORI.nii to D:\Saito\kaiseki221102\derivatives\ExploreASL\Population\rT1_ORI_sub-A07_1.nii
Combining transformations:
Segmentation transformation y_T1.nii of sub-A07_1

Running SPM job 'Deformations'
Done 'Deformations'
Done

Summarizing orientation parameters:
into: D:\Saito\kaiseki221102\derivatives\ExploreASL\sub-A07_1\xASL_qc_PrintOrientation_RigidRegT1.tsv
Collecting QC parameters...

ERROR: Structural module terminated for subject 7: sub-A07_1

ans =

'Unrecognized field name "qualityratings".
 
 Error in xASL_qc_CollectQC_Structural (line 83)
         Struct.T1w_IQR_Perc = min(100,max(0,105 - curr.S.qualityratings.IQR*10));
 
 Error in xASL_qc_CollectParameters (line 64)
     x = QCCollectFunction(x, iSubject);
 
 Error in xASL_wrp_VisualQC_Structural (line 111)
 x = xASL_qc_CollectParameters(x, iSubject, 'Structural');
 
 Error in xASL_module_Structural (line 490)
         xASL_wrp_VisualQC_Structural(x);
 
 Error in xASL_init_Iteration>runIteration (line 382)
 				[result, x] = jobfn(x); % [result, x] = jobfn(x, job_ex);
 
 Error in xASL_init_Iteration (line 125)
     [bAborted, xOut] = runIteration(dbSettings);
 
 Error in ExploreASL_Process (line 92)
         [~, x] = xASL_init_Iteration(x,'xASL_module_Structural');
 
 Error in ExploreASL (line 97)
         x = ExploreASL_Process(x);'

CONT: but continue with next iteration!

Job-iteration 7 stopped at 08-Nov-2022 13:19:06 and took 462 seconds
[�==============================================================================================]�

jan-petr Nov 8, 2022
Maintainer

Yes, v0.3.0 version of the GUI does go through multiple spawning of processes that execute the Import module. But it does so sequentially rather than in parallel, so this surprises me.

However, the upcoming v0.4.0 will take advantage of ExploreASL's v1.10.0 changes to its Import module (i.e. multiple contexts) and will therefore only spawn one process.

BTW: Version ExploreASL 1.10.0 should be available on 18Nov at latest.
The error above seems to be related with issue in CAT12 module saving of extra outputs and their use in quality check. Are you able to re-run the same without GUI? Are you able to share this example?

aso-toshihiko Dec 1, 2022
Author

Hi, is the next version going to be released in December?
Otherwise, it would be nice if there is some workaround for the issue by modifying CAT12. Because qCBF masked images are created, maybe it's just about PVC and ROI extraction, am I right?

aso-toshihiko Jan 31, 2023
Author

The current dev version produced the same error without GUI. Is there some fix needed to CAT12??

aso-toshihiko Feb 1, 2023
Author

Imported using ExploreASLJS.exe version 0.3.0 with an earlier dev version of 1.10 (because the GUI refuses the new 1.10.1 release.) without error.
Ran ExploreASL 1.10.1 from matlab: ExploreASL( 'D:\Saito\Results202301', [0 1 0], [1 1 0])

jan-petr · 2023-02-02T08:37:53Z

jan-petr
Feb 2, 2023
Maintainer

Dear Toshihiko, We have compiled the new version of ExploreASL 1.10.1 for Linux and Mac (Windows will be ready next week). Maurice - could there be an issue that the version is 1.10.1 and not 1.10.0? Toshihiko, I would recommend using ExploreASL 1.10.1 with GUI 0.4.0 https://github.com/MauricePasternak/ExploreASL-GUI/tags Regarding the longitudinal registration, I think this is similar to this issue: #1178 - we are working on this. Jan

…

* Imported using ExploreASLJS.exe version 0.3.0 with an earlier dev version of 1.10 (because the GUI refuses the new 1.10.1 release.) without error. * Ran ExploreASL 1.10.1 from matlab: ExploreASL( 'D:\Saito\Results202301', [0 1 0], [1 1 0]) image <https://user-images.githubusercontent.com/55236088/216052526-1e522329-36f6-41eb-aad1-e42d97f97ca8.png>

1 reply

aso-toshihiko Feb 2, 2023
Author

Thanks Jan!
Installing the GUI 0.4.0 seems challenging because it involves compiling JS.

Provide feedback

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Error by Unrecognized field name "STRUCT" #1232

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Error by Unrecognized field name "STRUCT" #1232

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aso-toshihiko Nov 7, 2022

Replies: 2 comments · 11 replies

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MDijsselhof Nov 7, 2022 Maintainer

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aso-toshihiko Nov 8, 2022 Author

SPM12: spm_coreg (v6435) 19:35:43 - 02/11/2022

SPM12: spm_coreg (v6435) 19:36:20 - 02/11/2022

SPM12: spm_reslice (v7141) 19:37:06 - 02/11/2022

Running SPM job 'Lesion filling'

Run lesion filling. Visit www.statistical-modeling.de/lst.html for updates and more information.

Working on image 1 out of 1 (100%) Finished successfully on 02-Nov-2022 19:44:55

CAT12.7-Beta r1615: 1/1: .\derivatives\ExploreASL\sub-A07_1\T1.n

CAT Preprocessing error for T1:

This is LST www.statistical-modeling.de/lst.html Algorithm: Compute total lesion volume Number of images to process: 1 Results are written to LST_tlv_0.05_20221102_205448.csv Progress 0.0%����100% Finished successfully on 02-Nov-2022 20:54:56

SPM12: spm_reslice (v7141) 20:54:59 - 02/11/2022

SPM12: spm_reslice (v7141) 20:55:08 - 02/11/2022

SPM12: spm_reslice (v7141) 20:55:13 - 02/11/2022

SPM12: spm_reslice (v7141) 20:56:01 - 02/11/2022

SPM12: spm_reslice (v7141) 20:56:08 - 02/11/2022

SPM12: spm_reslice (v7141) 20:56:16 - 02/11/2022

SPM12: spm_reslice (v7141) 20:56:22 - 02/11/2022

SPM12: spm_reslice (v7141) 13:11:29 - 08/11/2022

SPM12: spm_reslice (v7141) 13:11:36 - 08/11/2022

SPM12: spm_reslice (v7141) 13:11:40 - 08/11/2022

SPM12: spm_reslice (v7141) 13:12:20 - 08/11/2022

SPM12: spm_reslice (v7141) 13:12:26 - 08/11/2022

SPM12: spm_reslice (v7141) 13:12:33 - 08/11/2022

SPM12: spm_reslice (v7141) 13:12:37 - 08/11/2022

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jan-petr Nov 8, 2022 Maintainer

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aso-toshihiko
Nov 7, 2022

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MDijsselhof
Nov 7, 2022
Maintainer

aso-toshihiko Nov 8, 2022
Author

Run lesion filling. Visit www.statistical-modeling.de/lst.html
for updates and more information.

Working on image 1 out of 1 (100%)
Finished successfully on 02-Nov-2022 19:44:55

This is LST www.statistical-modeling.de/lst.html
Algorithm: Compute total lesion volume
Number of images to process: 1
Results are written to LST_tlv_0.05_20221102_205448.csv
Progress 0.0%��100%
Finished successfully on 02-Nov-2022 20:54:56

jan-petr Nov 8, 2022
Maintainer

aso-toshihiko Dec 1, 2022
Author

aso-toshihiko Jan 31, 2023
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aso-toshihiko Feb 1, 2023
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jan-petr
Feb 2, 2023
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aso-toshihiko Feb 2, 2023
Author