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Fixes #860 xASL_imp_DCM2NII & NII2BIDS: fix behavior for multiple anat files #861

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MichaelStritt merged 1 commit into from
Oct 2, 2021
Merged

Fixes #860 xASL_imp_DCM2NII & NII2BIDS: fix behavior for multiple anat files #861

MichaelStritt merged 1 commit into from
Oct 2, 2021

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@MichaelStritt MichaelStritt commented Sep 30, 2021

Linked issue

#860

@MichaelStritt MichaelStritt self-assigned this Sep 30, 2021
@MichaelStritt MichaelStritt added the import Related to data import module label Sep 30, 2021
@MichaelStritt MichaelStritt linked an issue Sep 30, 2021 that may be closed by this pull request
Multiple anatomical files exported by DCM2NIIX #860
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MichaelStritt commented Sep 30, 2021

Test with ADNI case

>> x = ExploreASL(pathTest,[1 1 0 1],0);
ExploreASL will run the import workflow and will load the dataset...
==============================================================================================
 ________                      __                                 ______    ______   __        
/        |                    /  |                               /      \  /      \ /  |      
########/  __    __   ______  ## |  ______    ______    ______  /######  |/######  |## |      
## |__    /  \  /  | /      \ ## | /      \  /      \  /      \ ## |__## |## \__##/ ## |      
##    |   ##  \/##/ /######  |## |/######  |/######  |/######  |##    ## |##      \ ## |      
#####/     ##  ##<  ## |  ## |## |## |  ## |## |  ##/ ##    ## |######## | ######  |## |      
## |_____  /####  \ ## |__## |## |## \__## |## |      ########/ ## |  ## |/  \__## |## |_____ 
##       |/##/ ##  |##    ##/ ## |##    ##/ ## |      ##       |## |  ## |##    ##/ ##       |
########/ ##/   ##/ #######/  ##/  ######/  ##/        #######/ ##/   ##/  ######/  ########/ 
                    ## |                                                                      
                    ## |                                                                      
                    ##/  

==================================== ExploreASL Settings =====================================
Dataset Root        ...M:\SoftwareDevelopment\MATLAB\m.stritt\Process_ADNI_3\output\006_S_4485
Import Modules      DCM2NII NII2BIDS BIDS2LEGACY
Process Modules     
bPause              False
iWorker             1
nWorkers            1
==============================================================================================
ExploreASL v1.8.0 initialized ... 
================================== DICOM to NIFTI CONVERSION =================================

Matching files (#=6):
sub-006S4485\session_1_2018-09-25_10_53_15.0\ASL\S729782
sub-006S4485\session_1_2018-09-25_10_53_15.0\FLAIR\S729786
sub-006S4485\session_1_2018-09-25_10_53_15.0\T1w\S729784
sub-006S4485\session_2_2019-10-01_11_40_18.0\ASL\S914718
sub-006S4485\session_2_2019-10-01_11_40_18.0\FLAIR\S914722
sub-006S4485\session_2_2019-10-01_11_40_18.0\T1w\S914720

Running DCM2NIIX...

...

================================== NIFTI to BIDS CONVERSION ==================================
Checking dataset_description.json ...
Missing recommended fields:           HEDVersion


====================================== CONVERT SESSION =======================================
Converting subject 006S4485, session 1, run 1 ...
Multiple anatomical NIfTIs exported by DCM2NIIX, automatically selecting the first one...
Scan sub-006S4485_ses-1_T1w ...
Multiple anatomical NIfTIs exported by DCM2NIIX, automatically selecting the first one...
Scan sub-006S4485_ses-1_FLAIR ...
Scan sub-006S4485_ses-1_asl ...

...

image

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MichaelStritt commented Sep 30, 2021

Minor flavor testing

I selected three flavors that have both ASL and T1w scans:

"flavorList": ["GE_PCASL_3Dspiral_14.0LX_1", "Philips_PCASL_3DGRASE_5.4.0.2_1", "Siemens_PCASL_3DGRASE_VE11C_2"]

BIDS conversion

================================== CHECK THE BIDS CONVERSION =================================
Dataset: GE_PCASL_3Dspiral_14.0LX_1
Dataset: Philips_PCASL_3DGRASE_5.4.0.2_1
Dataset: Siemens_PCASL_3DGRASE_VE11C_2

LEGACY conversion

================================= CHECK THE LEGACY CONVERSION ================================
Dataset: GE_PCASL_3Dspiral_14.0LX_1
Dataset:   derivativesReference
Missing:   \ExploreASL\bidsReportASL.json
Missing:   \ExploreASL\import_summary.csv
Missing:   \ExploreASL\xASL_module_Import.log

Dataset: Philips_PCASL_3DGRASE_5.4.0.2_1
Dataset:   derivativesReference
Missing:   \ExploreASL\bidsReportASL.json
Missing:   \ExploreASL\import_summary.csv
Missing:   \ExploreASL\xASL_module_Import.log

Dataset: Siemens_PCASL_3DGRASE_VE11C_2
Dataset:   derivativesReference
Missing:   \ExploreASL\bidsReportASL.json
Missing:   \ExploreASL\import_summary.csv
Missing:   \ExploreASL\xASL_module_Import.log

The comparison part seems to be a bit bugged, it shouldn't show the report and log files, but this isn't the fault of the changes within this branch. From my POV everything seems fine.

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MichaelStritt commented Sep 30, 2021 •
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@jan-petr: I'm not 100% sure if it's correct to just take the first one though. Maybe we have to merge them in some specific cases. For ADNI I'll probably just skip this session, since it's quite a lot of manual work to make it work for this rare case using the old v1.8.0 of ExploreASL.

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jan-petr approved these changes Oct 1, 2021
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OK. Can you check for this particular case if there are any differences between the two files? Parameters, absolute signal value, motion, etc? It would be good to know if the acquisition was done twice with a slightly different results or parameters, or if it was only saved twice and is otherwise identical...

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MichaelStritt commented Oct 2, 2021

OK. Can you check for this particular case if there are any differences between the two files? Parameters, absolute signal value, motion, etc? It would be good to know if the acquisition was done twice with a slightly different results or parameters, or if it was only saved twice and is otherwise identical...

I created a follow-up issue #866 and copied all the relevant text there.

@MichaelStritt MichaelStritt merged commit 6dc2766 into develop Oct 2, 2021
@MichaelStritt MichaelStritt deleted the import-#860_MultipleAnatFiles branch October 2, 2021 21:00
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Multiple anatomical files exported by DCM2NIIX

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