Fixes #732 Multi-Session support #753

MichaelStritt · 2021-08-02T15:49:42Z

Linked issue

Check out #732

Major changes

Move BIDS_fullPipelineTest.m to xASL_test_FullPipelineTest.m
Add studyPar option to xASL_io_ReadDataPar.m
Move xASL_bids_BIDS2Legacy.m to import module
Add underscore xASL_imp_DCM2NII_Subject.m
Rename xASL_imp_NII2BIDS_SubjectSession.m to xASL_imp_NII2BIDS_Session.m
Rename xASL_imp_NII2BIDS_SubjectSessionRun.m to xASL_imp_NII2BIDS_Run.m
... split functionality to ...RunAnat.m & ...RunPerf.m

Release notes

Cleaning code of DCM to BIDS import

MichaelStritt · 2021-08-02T16:02:01Z

Example

Okay, so we start with ADNI dataset 011_S_4105.

{"folderHierarchy":["^sub-(.+)$","^(session_\\d{1}).+$","^(ASL|T1w|M0|T2|FLAIR)$","S.+$"],
"tokenOrdering":[1,2,0,3],
"tokenVisitAliases":["session_1","1","session_2","2","session_3","3"
,"session_4","4","session_5","5","session_6","6","session_7","7"],
"tokenSessionAliases":["",""],
"tokenScanAliases":["^ASL$","ASL4D","^T1w$","T1w","^M0$","M0","^T2$","T2w","^FLAIR$","FLAIR"],
"bMatchDirectories":true}

We run the first import step...

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

==================================== ExploreASL Settings =====================================
Dataset Root        ...reDevelopment\MATLAB\m.stritt\Server_xASL\test_ADNI\test_out\011_S_4105
Import Modules      DCM2NII 
Process Modules     
bPause              False
iWorker             1
nWorkers            1
==============================================================================================
ExploreASL v1.8.0_BETA initialized ... 

Matching files:
    'sub-001\session_1_2013-07-26_15_10_24.0\ASL\S196762'
    'sub-001\session_1_2013-07-26_15_10_24.0\FLAIR\S196758'
    'sub-001\session_1_2013-07-26_15_10_24.0\T1w\S196752'
    'sub-001\session_2_2015-07-29_12_17_39.0\ASL\S267385'
    'sub-001\session_2_2015-07-29_12_17_39.0\FLAIR\S267396'
    'sub-001\session_2_2015-07-29_12_17_39.0\T1w\S267391'

#=6
Running import (i.e. dcm2niiX)
==============================================================================================
...

We get this temp directory structure ...

Then we run the second step of the import ...

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

==================================== ExploreASL Settings =====================================
Dataset Root        ...reDevelopment\MATLAB\m.stritt\Server_xASL\test_ADNI\test_out\011_S_4105
Import Modules      NII2BIDS 
Process Modules     
bPause              False
iWorker             1
nWorkers            1
==============================================================================================
ExploreASL v1.8.0_BETA initialized ... 
================================== dataset_description.json ==================================
Missing recommended fields:           HEDVersion

================================== BIDS JSON Check Results ===================================
Missing recommended ASL fields:       SliceEncodingDirection, AcquisitionVoxelSize, LabelingOrientation
The field ArterialSpinLabelingType is PASL, please check the dependencies below:
The following fields should be empty: LabelingDuration

================================== BIDS JSON Check Results ===================================
Missing recommended ASL fields:       SliceEncodingDirection, AcquisitionVoxelSize, LabelingOrientation
The field ArterialSpinLabelingType is PASL, please check the dependencies below:
The following fields should be empty: LabelingDuration

We get this rawdata directory structure for both visits ...

The we run the last import step and get ...

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

==================================== ExploreASL Settings =====================================
Dataset Root        ...reDevelopment\MATLAB\m.stritt\Server_xASL\test_ADNI\test_out\011_S_4105
Import Modules      BIDS2LEGACY
Process Modules     
bPause              False
iWorker             1
nWorkers            1
==============================================================================================
ExploreASL v1.8.0_BETA initialized ... 
Parsing BIDS scans: 100%
Note that any warnings may have only printed once if they were repeated for multiple scans
Always run your rawdata folder through the BIDS validator first and aim to avoid warnings
Converting from BIDS to Legacy: .\test_out\011_S_411100%
M0 parsed for .\test_out\011_S_4105\derivatives\ExploreASL\sub-001_2\ASL_1\ASL4D.nii.gz
Creating default dataPar.json since file was not found...
Overwriting x.dir.dataPar...

With this derivatives directory ...

Discussion

Overall I think the commits are quite clear and the changes make the code a lot more readable. Please don't let us overengineer here and let's try to get this merged until Wednesday. I'll run the FlavorDatabase later on, to see what kind of differences we get there.

HenkMutsaerts · 2021-08-02T16:10:20Z

I would do ses-001 instead of ses-1, like with sub-001

MichaelStritt · 2021-08-02T16:12:57Z

I would do ses-001 instead of ses-1, like with sub-001

That 1 comes directly from the aliases. We can do aliases that do this. According to BIDS things like plain text would be possible too though: https://bids-specification.readthedocs.io/en/stable/02-common-principles.html

HenkMutsaerts

Very nice work! Only some minor questions, and the general request to add comments. One hour of typing additional comments will help us (including you ;) a lot in the near future.

HenkMutsaerts · 2021-08-02T18:12:33Z

Functions/xASL_io_ReadDataPar.m

 % Copyright 2015-2021 ExploreASL

 %% Input Check
 if nargin < 1 || isempty(pathDataPar) || ~exist(pathDataPar, 'file')


If the first argument is not provided, it gives an error that the data par doesn't exist

Sure, easy fix: 4dbefa8 👍

HenkMutsaerts · 2021-08-02T18:14:09Z

Functions/xASL_io_ReadDataPar.m

 %
 % INPUT:
 %   pathDataPar     - Filename of the input parameter file with either .m or .json extension
+%   bDataPar        - Read JSON as dataPar.json (BOOLEAN, OPTIONAL, DEFAULT = true)


I would turn it around. If DataPar is the default, then the new option is bStudyPar. Default is off, and special case is to turn it on.

Sure, easy fix: 4dbefa8 👍

HenkMutsaerts · 2021-08-02T18:15:20Z

Functions/xASL_io_ReadDataPar.m


 	%% Check deprecated fields
-    x = xASL_io_CheckDeprecatedFieldsX(x,true);
+    if bDataPar


Seems as if this was done by default previously, is this needed for the studypar as well? Or did it previously just do nothing inside this function?

Do you remember the studyPar.json that Beatriz showed us yesterday? It had some of these basic fields that shouldn't be there and that were in a sub-structure. That's partially caused by xASL_io_CheckDeprecatedFieldsX, which was only recently added to xASL_io_ReadDataPar (#717).

Modules/SubModule_Import/xASL_imp_NII2BIDS.m

HenkMutsaerts · 2021-08-02T18:30:32Z

Modules/SubModule_Import/xASL_imp_NII2BIDS_Session.m

@@ -0,0 +1,71 @@
+function xASL_imp_NII2BIDS_Session(imPar, bidsPar, studyPar, listSessions, nameSubjectSession, bidsLabel, iSession)
+%xASL_imp_NII2BIDS_SubjectSession NII2BIDS conversion for a single sessions.


a single sessions -> a single session.
Also, add that this is a BIDS session and legacy visit.

Ah yes, fixed the other comments in the header too 9c36709 👍

HenkMutsaerts · 2021-08-02T18:37:56Z

Modules/SubModule_Import/xASL_imp_NII2BIDS_Session.m

+        sessionLabel = '';
+
+        % Only one session - no session labeling
+        if ~exist(fullfile(imPar.BidsRoot,['sub-' subjectLabel]),'dir')


Same as above. But I would always create a folder for sessions, that makes our life easier

Definitely agree, I answered above.

Now I understand. But disagree. My understanding was that BIDS encourages you not to create a ses subfolder when there is only a single session. So it makes your life easier, but goes against BIDS philosophy. We have this here, I would keep it.

Agree. BIDS philosophy makes it easier for users here. Sadly that comes with a little bit more work for the developers.

HenkMutsaerts · 2021-08-02T18:39:13Z

Modules/SubModule_Import/xASL_imp_NII2BIDS_Subject.m

+%   imPar               - JSON file with structure with import parameter (REQUIRED, STRUCT)
+%   bidsPar             - Output of xASL_imp_Config (REQUIRED, STRUCT)
+%   studyPar            - JSON file with the BIDS parameters relevant for the whole study (REQUIRED, STRUCT)
+%   nameSubjectSession  - name of the subject (REQUIRED, LIST)


LIST should be a cell structure right?

I think so, fixed it 088eadb 👍

HenkMutsaerts · 2021-08-02T18:39:36Z

Modules/SubModule_Import/xASL_imp_NII2BIDS_Subject.m


-    subjectLabel = xASL_adm_CorrectName(nameSubject,2);
+    % Make a subject directory
+    if ~exist(fullfile(imPar.BidsRoot,['sub-' bidsLabel.subject]),'dir')


Same as above

Same as above 088eadb 😄

HenkMutsaerts · 2021-08-02T18:41:26Z

Modules/SubModule_Import/xASL_imp_NII2BIDS_Subject.m

+    end
+
+    %% 2. Process the anat & perfusion files
+    listSessions = xASL_adm_GetFileList(fullfile(imPar.TempRoot,nameSubjectSession),'^ASL.+$',false,[],true);


Are we not mixing up sessions (visits) and runs (sessions) here? A list of sessions should in legacy be based on _1 _2 _3 etc., not on ASL.+

Yeah, this is a bit mixed up almost everywhere. It would be a lot easier if we had written down both notations for each function/section. This should be legacy visits I think (which is BIDS sessions) and there we have ASL_1 for visit 1 etc., right? I mean... it worked so far 😆

Nope, in legacy we have sessions (BIDS runs) ASL_1 ASL_2 ASL_3.
Also, in legacy we have visits (BIDS sessions) sub-001_1 sub-001_2 sub-001_3.

Yes. Agree. This is mixed up. But only the terminology is mixed up. It functions correctly...
We have used here in BIDS function the Legacy terminology. It is indeed incorrect to call it sessions, but it is treating it as runs, so we only need to change the names. I would do that in issue #775 - we already mention it there.

HenkMutsaerts · 2021-08-02T18:43:31Z

Modules/SubModule_Import/xASL_imp_NII2BIDS_Subject.m

        end
    end
+
+    bidsLabel.subject = xASL_adm_CorrectName(subjectName,2);


Are we sure here that we correct only the 'value' (for the keys sub- and ses-)? Or should this be done somewhere else to ensure that this is always the value?

Please also add a bit more comments, it's quite difficult to follow these scripts. I know that you're in a rush but this will backfire.

Like with a few other comments I have to say that this wasn't necessarily created in a rush. This was like this before and just moved. Before it was called nameSubject, but other than that we used the same correction function and everything. Adding more comments to code in general can be helpful though 😉
Regarding the specific functionality: I had to figure this out first too, but a simple debug made it super clear. We extract subject/visit from the name, so you could have something like sub-001_ses-1 or whatever and there we basically only want the 001 and the 1. We need to get rid of the hyphens and underscores, which is why we use xASL_adm_CorrectName. We did this exactly like this before though and was probably originally written by @jan-petr.

MichaelStritt · 2021-08-03T05:53:43Z

Full BIDS Pipeline Test

I just tested these six datasets and everything seems fine to me 😄

Dataset: GE_PCASL_3Dspiral_Product_pharma
Dataset: GE_PCASL_3Dspiral_volunteer
Dataset: Philips_PCASL_2DEPI_Bsup_AD1
Dataset: Philips_PCASL_3DGRASE_functional
Dataset: Siemens_PASL_2DEPI_ADNI2_B15_941_S_4764
Dataset: Siemens_PCASL_3DGRASE_AD

MichaelStritt · 2021-08-03T11:15:03Z

@HenkMutsaerts: I created the follow-up issues #754 & #755. Otherwise everything should be fine. We should focus on fixing #754 quickly.

HenkMutsaerts

Minor stuff left, nearly there!

HenkMutsaerts · 2021-08-04T13:33:48Z

Functions/xASL_bids_BIDS2Legacy.m

+%% 10. Create dataPar.json

 % Write DataParFile if it does not exist already
 if ~(xASL_exist(fullfile(pathLegacy, 'dataPar.json'),'file')==2)


You can change this into:

if ~xASL_exist(fullfile(pathLegacy, 'dataPar.json'), 'file')

so in Matlab you can omit the outer () brackets, and with 'file' you don't need to ask if it's equal to 2.

0d367c3 👍

HenkMutsaerts · 2021-08-04T13:34:28Z

Modules/SubModule_Import/xASL_imp_BIDS2Legacy.m



    %% 1. Input check
+    fprintf('================================== BIDS to LEGACY CONVERSION =================================\n');


LEGACY is our internal nomenclature, this has no meaning to the users, if you call it "ExploreASL legacy" this should be fine

HenkMutsaerts · 2021-08-04T13:35:48Z

Modules/SubModule_Import/xASL_imp_NII2BIDS_Session.m

+        if ~isempty(visitLabel)
+            sessionLabel = ['ses-' visitLabel];
+        else
+            sessionLabel = ['ses-' listSessions{iSession}(5:end)];


OK, if it's indeed iterating over sessions and not SubjectSession (what is very confusing as throughout the processing modules, we refer to SubjectSession as what is SubjectRun in BIDS... :)

Modules/SubModule_Import/xASL_imp_NII2BIDS_Session.m

HenkMutsaerts · 2021-08-04T13:37:24Z

Modules/SubModule_Import/xASL_imp_NII2BIDS_Session.m

+            xASL_adm_CreateDir(fullfile(imPar.BidsRoot,['sub-' subjectLabel],sessionLabel,'perf'));
+        end
+        inSessionPath = fullfile(imPar.TempRoot,nameSubjectSession,listSessions{iSession});
+        outSessionPath = fullfile(imPar.BidsRoot,['sub-' subjectLabel],sessionLabel);


Sure, but we don't get to see what the users do. So we only have to add a check later that it doesn't have twice sub- in the name, same for ses-.

HenkMutsaerts · 2021-08-04T13:38:44Z

Modules/SubModule_Import/xASL_imp_NII2BIDS_Subject.m

+    end
+
+    %% 2. Process the anat & perfusion files
+    listSessions = xASL_adm_GetFileList(fullfile(imPar.TempRoot,nameSubjectSession),'^ASL.+$',false,[],true);


Nope, in legacy we have sessions (BIDS runs) ASL_1 ASL_2 ASL_3.
Also, in legacy we have visits (BIDS sessions) sub-001_1 sub-001_2 sub-001_3.

HenkMutsaerts · 2021-08-04T13:40:11Z

Modules/SubModule_Import/xASL_imp_NII2BIDS_Subject.m


    % Get visitAliases from imPar
-    visitAliases = imPar.tokenVisitAliases(:,2);
+    if isfield(imPar,'tokenVisitAliases') && ~isempty(imPar.tokenVisitAliases) && size(imPar.tokenVisitAliases,2)>1


You can omit the ~isempty if you check for (size( , 2)>1

Doesn't hurt though...

it doesn't add anything. If it is empty, size()>1 will also return 0. So it is just extra time reading, would remove this.

Testing/xASL_test_FullPipelineTest.m

MichaelStritt · 2021-08-16T08:43:27Z

Current version

sourcedata...

DCM2NII

>> pathTest = 'M:\SoftwareDevelopment\MATLAB\m.stritt\Server_xASL\test_ADNI\test_out\011_S_4105';
>> x = ExploreASL(pathTest,[1 0 0 0],0);
ExploreASL will run the import workflow and will run the initialization...
==============================================================================================
 ________                      __                                 ______    ______   __        
/        |                    /  |                               /      \  /      \ /  |      
########/  __    __   ______  ## |  ______    ______    ______  /######  |/######  |## |      
## |__    /  \  /  | /      \ ## | /      \  /      \  /      \ ## |__## |## \__##/ ## |      
##    |   ##  \/##/ /######  |## |/######  |/######  |/######  |##    ## |##      \ ## |      
#####/     ##  ##<  ## |  ## |## |## |  ## |## |  ##/ ##    ## |######## | ######  |## |      
## |_____  /####  \ ## |__## |## |## \__## |## |      ########/ ## |  ## |/  \__## |## |_____ 
##       |/##/ ##  |##    ##/ ## |##    ##/ ## |      ##       |## |  ## |##    ##/ ##       |
########/ ##/   ##/ #######/  ##/  ######/  ##/        #######/ ##/   ##/  ######/  ########/ 
                    ## |                                                                      
                    ## |                                                                      
                    ##/  

==================================== ExploreASL Settings =====================================
Dataset Root        ...reDevelopment\MATLAB\m.stritt\Server_xASL\test_ADNI\test_out\011_S_4105
Import Modules      DCM2NII 
Process Modules     
bPause              False
iWorker             1
nWorkers            1
==============================================================================================
ExploreASL v1.8.0_BETA initialized ... 
================================== DICOM to NIFTI CONVERSION =================================

Matching files:
    'sub-001\session_1_2013-07-26_15_10_24.0\ASL\S196762'
    'sub-001\session_1_2013-07-26_15_10_24.0\FLAIR\S196758'
    'sub-001\session_1_2013-07-26_15_10_24.0\T1w\S196752'
    'sub-001\session_2_2015-07-29_12_17_39.0\ASL\S267385'
    'sub-001\session_2_2015-07-29_12_17_39.0\FLAIR\S267396'
    'sub-001\session_2_2015-07-29_12_17_39.0\T1w\S267391'

#=6
Running import (i.e. dcm2niiX)
...

temp data...

NII2BIDS

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

==================================== ExploreASL Settings =====================================
Dataset Root        ...reDevelopment\MATLAB\m.stritt\Server_xASL\test_ADNI\test_out\011_S_4105
Import Modules      NII2BIDS 
Process Modules     
bPause              False
iWorker             1
nWorkers            1
==============================================================================================
ExploreASL v1.8.0_BETA initialized ... 
================================== NIFTI to BIDS CONVERSION ==================================
================================== dataset_description.json ==================================
Missing recommended fields:           HEDVersion

Warning: The following user-defined/DICOM fields and DICOM-Phoenix fields differ:
  SoftwareVersions
================================== BIDS JSON Check Results ===================================
Missing recommended ASL fields:       SliceEncodingDirection, AcquisitionVoxelSize, LabelingOrientation
The field ArterialSpinLabelingType is PASL, please check the dependencies below:
The following fields should be empty: LabelingDuration

Warning: The following user-defined/DICOM fields and DICOM-Phoenix fields differ:
  SoftwareVersions
================================== BIDS JSON Check Results ===================================
Missing recommended ASL fields:       SliceEncodingDirection, AcquisitionVoxelSize, LabelingOrientation
The field ArterialSpinLabelingType is PASL, please check the dependencies below:
The following fields should be empty: LabelingDuration

rawdata...

BIDS2LEGACY

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

==================================== ExploreASL Settings =====================================
Dataset Root        ...reDevelopment\MATLAB\m.stritt\Server_xASL\test_ADNI\test_out\011_S_4105
Import Modules      BIDS2LEGACY
Process Modules     
bPause              False
iWorker             1
nWorkers            1
==============================================================================================
ExploreASL v1.8.0_BETA initialized ... 
============================ BIDS to ExploreASL LEGACY CONVERSION ============================
Parsing BIDS scans: 100%
Note that any warnings may have only printed once if they were repeated for multiple scans
Always run your rawdata folder through the BIDS validator first and aim to avoid warnings
Converting from BIDS to Legacy: 011_S_4105 1100%
M0 parsed for 011_S_4105 ASL4D.nii ...
M0 parsed for 011_S_4105 ASL4D.nii ...
Creating default dataPar.json since file was not found...
Overwriting x.dir.dataPar...

derivatives...

jan-petr

See the commits I made - they should all be minor.

See my answers. All can be resolved and/or moved to #775. So as far as I am concerned, we can merge.

Modules/SubModule_Import/xASL_imp_NII2BIDS.m

jan-petr · 2021-08-16T13:18:08Z

Modules/SubModule_Import/xASL_imp_NII2BIDS_Session.m

+        if ~isempty(visitLabel)
+            sessionLabel = ['ses-' visitLabel];
+        else
+            sessionLabel = ['ses-' listSessions{iSession}(5:end)];


Don't remember the history and we have to revamp this whole import to really use correctly sessions and not visits.

Here, obviously, if the visitLabel is missing, it extracts the visit from the session label by removing the first four characters (=="ses-") from the session label.

Again - the sessions/visit run methodology has to be unified for BIDS - I have created new issues for that in 1.9.0. #775

Modules/SubModule_Import/xASL_imp_NII2BIDS_Session.m

jan-petr · 2021-08-16T13:38:30Z

Modules/SubModule_Import/xASL_imp_NII2BIDS_Session.m

+            xASL_adm_CreateDir(fullfile(imPar.BidsRoot,['sub-' subjectLabel],sessionLabel,'perf'));
+        end
+        inSessionPath = fullfile(imPar.TempRoot,nameSubjectSession,listSessions{iSession});
+        outSessionPath = fullfile(imPar.BidsRoot,['sub-' subjectLabel],sessionLabel);


Good point - let's make a new issue for that. Or rather lets glue that to #775 (I've just done that).

jan-petr · 2021-08-16T13:40:22Z

Modules/SubModule_Import/xASL_imp_NII2BIDS_Session.m

+        sessionLabel = ['_' sessionLabel];
+    else
+        % Session label is skipped
+        sessionLabel = '';


Not really understand the issue here. Yes - let's add to #775.

jan-petr · 2021-08-16T13:42:11Z

Modules/SubModule_Import/xASL_imp_NII2BIDS_Session.m

+        sessionLabel = '';
+
+        % Only one session - no session labeling
+        if ~exist(fullfile(imPar.BidsRoot,['sub-' subjectLabel]),'dir')


Now I understand. But disagree. My understanding was that BIDS encourages you not to create a ses subfolder when there is only a single session. So it makes your life easier, but goes against BIDS philosophy. We have this here, I would keep it.

jan-petr · 2021-08-16T13:47:56Z

Modules/SubModule_Import/xASL_imp_NII2BIDS_Subject.m

+    end
+
+    %% 2. Process the anat & perfusion files
+    listSessions = xASL_adm_GetFileList(fullfile(imPar.TempRoot,nameSubjectSession),'^ASL.+$',false,[],true);


Yes. Agree. This is mixed up. But only the terminology is mixed up. It functions correctly...
We have used here in BIDS function the Legacy terminology. It is indeed incorrect to call it sessions, but it is treating it as runs, so we only need to change the names. I would do that in issue #775 - we already mention it there.

In the studyPar we should not do the deprecated fields moving that we do for the dataPar.json. This fix is related to issue #752.

…odality behavior

…ulti-session

ghost · 2021-08-24T12:15:57Z

Hello ExploreASL experts,

Previously, I have performed ExploreASL on OASIS datasets by keeping manually prepared subjects folder inside the analysis folder using version 1.5.1. I was able to run 5-6 subjects simultaneously. For the ADNI dataset, can you please inform me what major changes I need to make to run the ExploreASL on a group of subjects? Will the convert to source options work if I place several subjects with label files inside the ADNI folders?

Thanks for your support and consideration.

Regards,
Anindita

MichaelStritt added the bids Moving ExploreASL to BIDS compatibility label Aug 2, 2021

MichaelStritt self-assigned this Aug 2, 2021

MichaelStritt requested a review from HenkMutsaerts August 2, 2021 16:02

MichaelStritt linked an issue Aug 2, 2021 that may be closed by this pull request

NII2BIDS Convert visits to BIDS sessions #732

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HenkMutsaerts requested changes Aug 2, 2021

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MichaelStritt requested a review from HenkMutsaerts August 3, 2021 05:54

MichaelStritt mentioned this pull request Aug 3, 2021

Optimization of the import #755

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ExploreASL deleted a comment from MichaelStritt Aug 3, 2021

HenkMutsaerts requested changes Aug 4, 2021

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MichaelStritt requested a review from HenkMutsaerts August 4, 2021 14:07

MichaelStritt assigned BeatrizPadrela and unassigned MichaelStritt Aug 4, 2021

HenkMutsaerts assigned MichaelStritt and unassigned BeatrizPadrela Aug 4, 2021

MichaelStritt linked an issue Aug 16, 2021 that may be closed by this pull request

Generalize testing #751

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MichaelStritt requested a review from jan-petr August 16, 2021 11:07

MichaelStritt removed a link to an issue Aug 16, 2021

Generalize testing #751

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jan-petr approved these changes Aug 16, 2021

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HenkMutsaerts and others added 6 commits August 16, 2021 16:46

#732 xASL_imp_DCM2NII*: Fix legacy _ visits separator

b7b813f

#732 Read studyPar.json correctly

4d5262e

In the studyPar we should not do the deprecated fields moving that we do for the dataPar.json. This fix is related to issue #752.

#732 xASL_imp_NII2BIDS: Overall simplification for multi-session support

180fcac

#732 xASL_imp_NII2BIDS_Run: rename from subjectsessionrun, simplify m…

3381d70

…odality behavior

#732 xASL_imp_NII2BIDS_RunAnat: NII2BIDS only anat files

0cb7f76

#732 xASL_imp_NII2BIDS_RunAnat: NII2BIDS only perf files

5bb58a3

MichaelStritt and others added 12 commits August 16, 2021 16:46

#732 xASL_imp_NII2BIDS_(...): remaining required script changes for m…

ff07c4e

…ulti-session

#732 xASL_io_ReadDataPar: bDataPar -> bStudyPar

04042cf

#732 xASL_imp_NII2BIDS_Session: remove exist and fix header

fd01a63

#732 xASL_imp_NII2BIDS_Subject: fix header and exist

ddb2514

#732 xASL_imp_NII2BIDS_Subject: fix bug related to missing field

5e4c087

#732 Design: minor cosmetics & reduce verbosity

5642ff6

#732 xASL_test_FullPipelineTest: add testConfig JSON

efb56c2

#732 xASL_imp_NII2BIDS: bStudyPar

ead9f32

#732 xASL_..._BIDS2Legacy: minor improvements and fix printing

b1253fe

#732 .gitignore: testConfig.json can have suffixes

aba7a2e

#732 xASL_io_ReadDataPar: Cosmetics

7af8176

#732 xASL_imp_NII2BIDS_Session: Minor change in directory creation

dccbdcf

MichaelStritt force-pushed the bug-#732_NIIvisits2BIDSsessions branch from 1f52e94 to dccbdcf Compare August 16, 2021 14:47

MichaelStritt merged commit dccbdcf into develop Aug 16, 2021

MichaelStritt deleted the bug-#732_NIIvisits2BIDSsessions branch August 16, 2021 14:48

		@@ -0,0 +1,71 @@
		function xASL_imp_NII2BIDS_Session(imPar, bidsPar, studyPar, listSessions, nameSubjectSession, bidsLabel, iSession)
		%xASL_imp_NII2BIDS_SubjectSession NII2BIDS conversion for a single sessions.



		%% 1. Input check
		fprintf('================================== BIDS to LEGACY CONVERSION =================================\n');

Fixes #732 Multi-Session support #753

Fixes #732 Multi-Session support #753

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MichaelStritt commented Aug 3, 2021

Full BIDS Pipeline Test

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MichaelStritt commented Aug 2, 2021 •

edited by jan-petr

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MichaelStritt commented Aug 2, 2021 •

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