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MRI File Manager

MRI File Manager allows the reading of some raw and processed data files from MRI Spectrometers :

- Bruker Paravision PV5, PV6 & PV7 (raw data of magnitude type).
- Dicom from Bruker, Philips, Siemens.
- Philips Achieva (Par/Rec v4, v4.1 & v4.2, Xml/Rec v5).
- Nifti-1 (with or without Json).
- BIDS - Brain Imaging Data Structure.

It also allows for converting MRI images to Nifti-1 or BIDS:

- Export MRI data in Nifti-1 or BIDS format until 5 dimensions of the image (x, y, slice, frame, temporal).
- Json files are created and associated with Nifti files in order to contain MRI parameters.
- an option of anonymization allows to hide sensitive informations about the patient (name, age, sex, weight).
- adaptation of orientation information in Nifti headers (tested on SPM, FSL and MRtrix).
- option of customizing the Nifti file names.
- possibility to create text files containing bvecs & bvals for MRtrix and FSL (Bruker, Dicom and Philips).

Documentation

The documentation is available on mri_conv's website here: https://populse.github.io/mri_conv.
To download the latest 'development' version, click here or 'Download ZIP' in 'Clone or download'.

Release history

05/09/2023: version 23.4.2a
Features modified:
    - bvec, bval : now bvec and bval files have .bvec and .bval extensions (FSL format). The Mrtrix format stay as before (.txt) 

29/08/2023: version 23.4.1a
Features added:
    - Bids : when exporting to Nifti, a 'bvec_bval' tag is added to the LogExport. Its value is 'yes' if bvec/bval files have been copied.

25/08/2023: version 23.4.0a
Features added:
    - Bids : now possibility to read json generated by dcm2niix
    - Bids : for diffusion, now bids export copies bvec/bval files in the same folder as the Nifti/json pair

26/06/2023: version 23.3.0a
Bug fixed:
    - Dicom : problem with bvec/bval for some Dicom solved
Others:
    - some fields added in DictionaryMRI_System.yml : Slice_Gap, Slice Thickness In Acq. 

05/04/2023: version 23.2.0a
Features added:
    - all : 'Directory' field added in the naming choice for exporting files to Nifti
Others:
    - ImageJ : update to version 1.54d

01/02/2023: version 22.2.2a
Bug fixed:
    - Bruker : problem of bvec/bval generation (when the number of diffusion experiments >1) solved

13/09/2022: version 22.1.9a
Bug fixed:
    - Dicom : normalization problem fixed 

04/05/2022: version 22.1.8a
Bug fixed:
    - Dicom Bruker: normalization problem fixed 

22/04/2022: version 22.1.7b
Bug fixed:
    - Dicom : image order problem with some Dicom files (with dicomdir) fixed

20/04/2022: version 22.1.7a
Bug fixed:
    - Dicom : image order problem with some Dicom files fixed

23/03/2022 : version 22.1.6a
Bug fixed:
    - Dicom : image order problem for some Philips DICOM files (SWIp) fixed
    - ImageJ : some plugins added (Input_Output, niftijio.jar)

11/03/2022 : version 22.1.5a
Bug fixed:
    - Dicom : affine transformation correction (for some SPECT files) 

18/02/2022 : version 22.1.4a
Bug fixed:
    - Dicom : problem reading some 2D DICOM files fixed
    - Philips : problem reading some scanning sequences fixed

03/02/2022 : version 22.1.3a
Bug fixed:
    - Dicom : registration problem with some DICOM files fixed (new Slice Thickness calculation method)
Others:
    - ImageJ : update to version 1.53o

01/02/2022 : version 22.1.2a
Bugs fixed:
    - Dicom : problem reading some DICOM files fixed

28/01/2022 : version 22.1.1a
Bugs fixed:
    - Basket : wrong file size
Others:
    - basket : the bottom list is replaced by a table (now possibility to sort)

19/01/2022 : version 21.8.2a
Bugs fixed:
    - All : wrong value displayed in 'Image in Acquisition' field fixed
    - BIDS : export bugs to Nifti/Json fixed
    - Dicom : some dicom file reading errors fixed      
Features added:
    - Dicom & BIDS : icons displayed in the file dialog
    - ImageJ : plugIn CEST added

14/09/2021 : version 21.7.1a
Bugs fixed:
    - Philips : problem with bvec, bval files fixed
Features added:
    - Dicom : export to Nifti in windowless mode
Other:
    - ImageJ : update to version 1.53j, some plugins removed

18/05/2021 : version 21.6.1a
Bugs fixed:
    - Bruker : problem of opening 32bits float type images solved (Bruker360)
    - All : the naming of files exported to BIDS (when adding all sequences to basket) corrected

04/05/2021 : version 21.5.1a
Features added:
    - Bruker : now compatibility with Paravision360
Other:
    - All : the export to BIDS by default is now as sub-(PatientName)/ses-(AcquisitionDate)/(BIDSmodality)/sub-(PatientName)_ses-(AcquisitionDate)_(SequenceName).nii

14/04/2021 : version 21.4.1a
Bugs fixed:
    - Dicom : image order problem with some Dicom JpegLossLess fixed

09/04/2021 : version 21.3.1a
Bugs fixed:
    - Dicom : bug with some DICOM files fixed
    - Philips : image order problem with some 5D file resolved
Features added:
    - All : more information in error messages (Class)

12/02/2021 : version 21.2.0a
Bugs fixed:
    - Dicom : bvec and bval calculation errors corrected

13/01/2021 : version 21.1.0a
Others:
  - Dicom : bvec and bval extraction conforms to dcm2nii

19/11/2020 : version 20.2.8b
Bugs fixed:
  - Nifti : bug when adding Nifti without json to basket fixed 
  - the 'help' menu didn't work
Others:
  - the dot character '.' is replaced by underscore '_' in the naming of files to export to Nifti

14/10/2020 : Version 20.2.7a
Bugs fixed:
  - Bruker : in windowless mode, export to Nifti with multiple orientation (axia, coronal, sagittal) is now possible.
  - Philips : in windowles mode, naming when exporting to Nifti improved.

14/10/2020 : Version 20.2.6a
Bugs fixed:
  - Dicom: Image Dicom option forced to 'ignore Rescale Slope'
Others:
  - ImageJ update to 1.53e

16/09/2020 : Version 20.2.5a
Bugs fixed:
  - bug when export to Nifti in windowless mode with 'bvecs, bvals' option enabled fixed
Others:
  - bvecs and bvals can be added in json file if 'bvecs, bvals' option enabled (with field name 'bvecs' and 'bvals').

11/09/2020 : Version 20.2.4b
Bugs fixed:
  - Bruker : bug with some 3D image when nslice=1 (IRMOD) fixed.

10/09/2020 : Version 20.2.4a
Bugs fixed:
  - Bruker : bug with 4D image when nslice=1 fixed.

10/09/2020 : Version 20.2.3c
Modification :
  - some graphics improvements
Others:
  - ImageJ update to 1.53d
  - ImageJ : 3D plug-in added

10/08/2020 : Version 20.2.3b
Modification :
  - ImageJ : absolute path of ImageJ (instead of relative)
Others:
  - JTattoo update to 1.6.13
  - removal of some unnecessary plugins from ImageJ

17/07/2020 : Version 20.2.3a
Bugs fixed:
  - Bruker : bug with normalization for some parametrics 3d sequence fixed.

03/07/2020 : Version 20.2.2a
Bugs fixed:
  - Basket manager : bug with the combobox "Nifti-1 , BIDS" fixed.

01/07/2020 : Version 20.2.1a
Bugs fixed:
  - Philips : bug with the 'history' field under the buttons fixed.
Others:
  - ImageJ update to 1.53c

24/06/2020 : Version 20.2.0a
Features added:
  - Philips : now compatible with ParRec V4 and V4.1.
          possibility to select a single directory containing Philips data.
Bugs fixed:
  - DICOM : problem reading some Dicom files (16 bits signed) fixed.
Others:
  - ImageJ update to 1.53b

18/06/2020 : Version 20.1.5d
Bugs fixed:
  - Dicom Philips : image order problem in some sequences 4D fixed.

12/06/2020 : Version 20.1.5c
Bugs fixed:
  - Bruker : bug with 'slice package' fixed

14/05/2020 : Version 20.1.5b
Bugs fixed:
  - Bruker : bug when exporting to Nifti with number of slice = 1 fixed
  - Philips xml/REC : display bug when opening xml file fixed

17/04/2020 : Version 20.1.4b
Modification:
  - some graphic improvements
Others:
  - dependencies update

15/04/2020 : Version 20.0.4b
Bug fixed:
  - Bruker: slice thickness in Nifti header for Localizer/Tripilot sequence corrected
Modification:
  - The combobox of file history is now under the buttons "Bruker","Dicom" etc...
Others:
  - ImageJ update to 1.52v

09/04/2020 : Version 20.0.3b
Modification:
  - Option export window: modification of tab "Nifti naming"

08/04/2020 : Version 20.0.2b
Bug fixed:
  - Basket manager : bug under Windows when filling the basket fixed

08/04/2020 : Version 20.0.2a
Features added:
  - Basket manager : preview window added
  - Export to BIDS : better compatibility with modalities

30/03/2020 : Version 20.0.1a
Features added:
  - All : now possibility to export Bruker, Philips and Dicom in BIDS format (still in development)
  - Bruker : affine transformation now compatible with MRTrix
Bug fixed:
  - Nifti: problem exporting Nifti files without JSON fixed

06/09/2019 : Version 19.6.1a
Features added:
  - Philips : possibility to launch MRI File Manager by script in windowless mode (see section 'Launching of the software' in 'Installation' page).
Bug fixed:
  - Philips: image order problem in some sequences 5D fixed.

29/08/2019 : Version 19.6.0a
Features added:
  - Bruker : possibility to launch MRI File Manager by script in windowless mode (see section 'Launching of the software'    in 'Installation' page).
  - Bids : menus "see 'dataset_description.json' file" and "see 'participants.tsv' file" added in popup menu.
Bug fixed:
  - Dicom Philips: image order problem in some sequences 5D fixed.

09/08/2019 : Version 19.5.6a
Bug fixed:
  - Bids : some bugs who crashed Populse_mia fixed.

09/08/2019 : Version 19.5.5a
Others:
  - Bids : following the Bids development, now possibility to export Bids structures to Nifti .

09/07/2019 : Version 19.5.4b
Features added:
  - Bids : following the Bids development(still in trial version).

05/07/2019 : Version 19.5.3b
Features added:
  - Bids - Brain Imaging Data Structure: new MRI file format introduced in the software (still in trial version).

02/07/2019 : Version 19.4.3b
Bug fixed:
  - DICOM: problem reading some Dicom files.

02/07/2019 : Version 19.4.3a
Features added :
  - DICOM (Philips): possibility to generate bvecs/bvals files for reading of diffusion in MRtrix or FSL.
Others:
  - best display of JSON text in log
  - best display of no-isotropic images in thumbnail list

25/06/2019 : Version 19.3.3a
Bugs fixed:
  - Bruker : affine transformation problem of some Bruker sequences fixed.
  - NIFTI : problem reading some Nifti files (64 bits float) fixed.
  - Philips : problem reading when sequences had same number serial, protocol, acquisition time ... fixed.

21/06/2019 : Version 19.3.2a
Bugs fixed:
  - NIFTI : problem reading some Nifti files (16 bits unsigned) fixed.
  - Philips : problem reading when files had lowercase extensions (*.rec, *.par) fixed.
Features added :
  - Philips : possibility to generate bvecs/bvals files for reading of diffusion by MrTrix and FSL.

12/06/2019 : Version 19.3.1a
Bugs fixed:
  - DICOM : problem reading Dicom files without rescale slope and intercept

06/06/2019 : Version 19.3.0a    
Bugs fixed:
  - DICOM : dimension reversed for some Dicom.
  - problem of the dialogue window 'Loading thumbnail ...' that did not always close resolved
Features added :
  - Bruker : possibility to generate bvecs/bvals files for reading of diffusion by MrTrix 
    (see page 'Documentation', section 'Set options')
  - add option [ProjectsDir] for the script (see page 'Installation', section 'Launching of the software')
Others:
  - Json Irmage : now, all parameters that have floating or integer values (same single) are presented as an array (list of list)
  - better management of items in the basket
  - exit code = 100 (for populse_mia project only)

04/04/2019 : Version 19.2.3a
Bugs fixed:
  - DICOM : for some Dicomdir files, anonymization did not work.
  - Nifti : anonymization did not work
  - Bruker : "Sequence Name" tag more complete for parametric images

03/04/2019 : Version 19.2.2a
Bugs fixed:
  - DICOM : for some Dicom files, anonymization did not work.
  - DICOM : after the ImageJ upgrade to 1.52n, some DICOM images were not displayed in the 'thumbnails' area.
Others:
  - ImageJ update to 1.52n

04/03/2019 : Version 19.2.1a
Bugs fixed:
  - DICOM : problems opening Dicom files which included the same serial number.
  - PHILIPS : problem opening DwiSE images.
Features added :
  - DICOM : add in "Preference" menu the option "simplified view for DICOMDIR" for faster reading. 
Others:
  - a new column 'Note' added in the 'Data browser' table.
  - a new column 'Serial Number' added in the 'MRI sequence' table.

22/01/2019 : Version 19.0.0a
Bugs fixed:
  - DICOM : problem opening Dicom files which are located in a root directory of a disk.

11/12/2018 : Version 18.2.9a
Bugs fixed:
  - PHILIPS : under Linux, display problem for Xml/Rec files.
Others:
  - 'DataAnonymized' tag modified in json file (add 'Description, 'format', ...).

11/12/2018 : Version 18.2.8a
Bugs fixed:
  - better research of Nifti files.
Features added :
  - options to anonymize MRI datas ->  'DataAnonymized' tag added in json file (value = no or yes).
  - BRUKER : possibility to export the parametric images separatly (see 'File'-> export -> Option export' menu).

04/12/2018 : Version 18.1.8a
Bugs fixed:
  - problem with export to Nifti (Populse_MIA)
  - problem with defaut directory for the exported data.
Others:
  - the software version is displayed at the top of the sofwtare window.
  - DictionaryMRI_System.yml is modified ('Patient Weight', type = string instead float)
  - PHILIPS: 'Patient Sex', 'Patient Weight', 'Patient BirthDate' tags added.