Bug #713 structural module error by jan-petr · Pull Request #716 · ExploreASL/ExploreASL

jan-petr · 2021-07-07T18:59:03Z

Linked issue

MichaelStritt · 2021-07-08T07:03:34Z

I think I found my main bug. Within xASL_init_DataLoading I'm doing the loading of the dataPar.json, just like we normally did. So there we call xASL_init_LoadDataParameterFile. Within xASL_init_LoadDataParameterFile we read in x.D.ROOT.
In ExploreASL_Initialize before xASL_init_DataLoading, however, we run xASL_init_DefinePaths. This doesn't seem to be data independent at all, since it runs xASL_init_DefinePaths which itself requires x.D.ROOT.
The other bug is in xASL_init_checkDatasetRoot, which turns off data loading if there is no dataPar.json within derivatives yet. That one can be fixed a little bit easier I think.

MichaelStritt · 2021-07-08T11:08:26Z

Philips_2DEPI_FLAIRsegmentation_PWI4D_QuantificationParameters_LoQ

These things can be fixed quite easily 👍

Fix 1: https://github.com/ExploreASL/TestDataSets/commit/2b0d792a2de119096287fee0b342879c45b5260c

Fix 2: https://github.com/ExploreASL/TestDataSets/commit/e4454d4f1481d8226f451991f378a1e3f8ff0c0e

MichaelStritt · 2021-07-08T12:10:31Z

Bug that Jan discovered already

------------------------------------------------------------------------
CAT Preprocessing error for T1:
------------------------------------------------------------------------
Reference to non-existent field 'YlesionFull'.
------------------------------------------------------------------------
  611 - 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
  378 - xASL_module_Structural
  394 - runIteration
  100 - xASL_Iteration
   43 - ExploreASL_ProcessMaster
   82 - ExploreASL_Master
  340 - xASL_qc_TestExploreASL
------------------------------------------------------------------------

Print 'Graphics' figure to: 
  .\Philips_2DEPI_Lesion_NoFLAIR_NoM0_HiQ\Sub-0001\report\catreport_SPM12.pdf
  Remove ".\Philips_2DEPI_Lesion_NoFLAIR_NoM0_HiQ\Sub-0001\mri\p1T1.nii" 
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 ".\Philips_2DEPI_Lesion_NoFLAIR_NoM0_HiQ\Sub-0001\mri\p2T1.nii" 
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 ".\Philips_2DEPI_Lesion_NoFLAIR_NoM0_HiQ\Sub-0001\mri\p0T1.nii" 
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!
...

Hopefully fixed in 9626dbb

BeatrizPadrela

Works on afivasc data!

MichaelStritt · 2021-07-09T07:55:29Z

Test datasets

MichaelStritt · 2021-07-09T08:34:54Z

BIDS conversion test

Pipeline

Only one error and as far as I know that one was there before because the image was zeroed out?

Philips_PCASL_3DGRASE_functional
3D_GRASE sequence detected
ERROR: ASL module terminated for subject 1: sub-Patient1
ans =
Error using xASL_module_ASL line 220
Invalid ASL image

HenkMutsaerts

Looks good!

HenkMutsaerts · 2021-07-09T10:22:03Z

@MichaelStritt continues deserving more beer. Be careful not to work too hard or you'll be very drunk at the ExploreASL workshop in September ;)

…reASL always uppercase, remove 1

jan-petr and others added 3 commits July 7, 2021 19:43

#713 Fix directory errors in initialization

c5e8e26

#713 xASL_qc_PCPStructural: Fix mask data type issue

657fae7

#713 MapsAdded UINT16->UINT8

c230c39

jan-petr requested review from BeatrizPadrela, HenkMutsaerts, MDijsselhof and MichaelStritt July 7, 2021 18:59

jan-petr self-assigned this Jul 7, 2021

jan-petr linked an issue Jul 7, 2021 that may be closed by this pull request

Structural module: matrices multiplication is not working #713

Closed

#713 Fix masking with UINT8 images

3c445d4

MichaelStritt and others added 6 commits July 8, 2021 09:31

#713 x.D.ROOT fix

1fc333e

#713 Correct merging of structs

246c568

#713 Backwards compatibility

2db86c0

#713 xASL_im_SkullStrip fix UINT8 error

0a3cec7

#713 Backwards compatibility (minor improvements)

c24203e

#713 Fix qc testing on windows

38b8f7b

MichaelStritt added 4 commits July 8, 2021 14:26

#713 Fix reference TSV data for shortened test case name

a70878b

#713 xASL_io_Nifti2Im: Load as single on default

9626dbb

#713 xASL_io_Nifti2Im: Fix input parsing

655c951

#713 xASL_qc_TestExploreASL: Minor fix testing script

090ffa6

MichaelStritt added the bug Something isn't working label Jul 8, 2021

#713 xASL_qc_TestExploreASL: Fix path related issue for TC coefficients

7330d7a

MichaelStritt approved these changes Jul 9, 2021

View reviewed changes

BeatrizPadrela approved these changes Jul 9, 2021

View reviewed changes

HenkMutsaerts approved these changes Jul 9, 2021

View reviewed changes

MichaelStritt assigned MichaelStritt and unassigned jan-petr Jul 9, 2021

MichaelStritt removed the request for review from MDijsselhof July 9, 2021 10:31

MichaelStritt assigned jan-petr and unassigned MichaelStritt Jul 9, 2021

HenkMutsaerts and others added 2 commits July 9, 2021 12:39

#707 xASL_init_checkDatasetRoot: minor fix derivatives path check

80da425

#707 xASL_init_checkDatasetRoot: derivatives always lowercase, Explo…

94a42c7

…reASL always uppercase, remove 1

jan-petr force-pushed the develop branch from 7a5d3cd to cdc07e1 Compare July 9, 2021 10:42

jan-petr merged commit 94a42c7 into develop Jul 9, 2021

jan-petr deleted the bug-#713_StructuralModuleError branch July 9, 2021 10:45

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Bug #713 structural module error#716

Bug #713 structural module error#716
jan-petr merged 17 commits intodevelopfrom
bug-#713_StructuralModuleError

jan-petr commented Jul 7, 2021

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jan-petr commented Jul 7, 2021

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Philips_2DEPI_FLAIRsegmentation_PWI4D_QuantificationParameters_LoQ

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Bug that Jan discovered already

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MichaelStritt commented Jul 9, 2021

Test datasets

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BIDS conversion test

Pipeline

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HenkMutsaerts commented Jul 9, 2021

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MichaelStritt commented Jul 8, 2021 •

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