function dicom_sort_convert_main(varargin)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% dicom_sort_convert_main.m
% - creates directory structure and converts to ANALYZE or NIfTI
%
% Simon Robinson. 15.6.2010
% Latest Version: v1.17
% : v1.14 9.1.2009
% : v1.13 1.12.2008
% : v1.12 21.10.2008
% : v1.8 1.8.2007
% : v1.6 30.3.2007
% : v1.5 17.1.2007
% : v1.4 16.1.2007
% : v1.3 20.12.2006
%
% Widget-based
% Usage: (GUI) dicom_sort_convert_main
% : (script) dicom_sort_convert_main(data)
%
% see
%
% Writes an activity log "dicom_sort_convert_log.txt" to the writefile directory selected. Error
% messages and warnings should be written here. Check in the event of
% problems.
%
% Also writes acquisition information (TR/TE etc) in "text_header.txt" in each scan
% directory %
%
% Functions called, written by other groups
%cbiReadNifti(readfile, {[],[],[(i-1)*d4+1 i*d4],[]});
% MGH Freesurfer Toolbox
%
% isdicomfile.m
% defmossize.m
% mos2vol.m
% mossub2volsub.m
% mosind2volind.m
%
% NIfTI toolbox - Jimmy Shen -
% http://www.mathworks.com/matlabcentral/fileexchange/loadFile.do?objectId=8797&objectType=File
%
% workbar.m -
% Daniel Claxton - % http://www.mathworks.com/matlabcentral/fileexchange/loadFile.do?objectId=7109&objectType=file
%
% GUI data:
% data.default_startpath =
% data.readfile_dir = unsorted data directory
% data.writefile_dir_selected = the writefile directory selected by user
% data.writefile_dir = writefile_dir_selected appended by dicom/analyze
% data.current_dir = current directory to write to
% data.current_scan = scan series being processed
% data.current_readfile_stem = stem for current scan series
% data.first_scan = 'yes'/'no'
% data.readfile_filter = '*.IMA' (could be set to '*.dcm')
% data.flist = a list of files to be copied/converted
% data.fsublist = a list of the files to be copied/converted in current scan
% data.NFullstopsPrior = how many full stops before the scan number? - set in select_sort_and_convert_Callback.m
% data.retain_dicom = 'no'/'yes'
% data.scanlistonly = 'yes'/'no'
% data.fp_scanlist ; file pointer of scan list file
% data.log_style = 'verbose'/'normal' ; set to 'verbose' in test mode ;% not currently used
% data.warning_present = 'yes'/'no'
% data.warning_text = a string into which all warnings are concatenated;
% data.convert = 'yes'/'no'
% data.convert_format = 'nift'/'analyze'
% data.current_conversion = 'dicom'/'convert'/'list'
% data.current_readfile_example ; first file in each scan dir
% data.current_dcminfo; dcminfo for first file in scan dir
% data.current_nfiles ; number of files in current scan
% data.current_writefile_th ; text header for current scan
% data.current_mosaic_flag ; mosaic flag for current scan
% data.current_header_pars ; header pars for current scan
% data.current_header_pars.dim_FOV_phase = dim_FOV_phase;
% data.current_header_pars.dim_FOV_read = dim_FOV_read;
% data.current_header_pars.dim_VS_phase = dim_VS_phase;
% data.current_header_pars.dim_VS_read = dim_VS_read;
% data.current_header_pars.dim_nslices = dim_nslices;
% data.current_header_pars.nechos = nechos;
% data.current_header_pars.echo_times = echo_times;
% data.current_header_pars.dim_phase = dim_phase;
% data.current_header_pars.dim_read = dim_read;
% data.current_header_pars.dim_slice_thick = dim_slice_thick;
% data.current_header_pars.PE_dir ; 'ROW' or 'COL'
% data.current_header_pars.rescaled = 'yes'/'no';
% data.current_header_pars.rescale_intercept
% data.current_header_pars.rescale_slope
% data.current_analyze_struct ; analyze structure for current scan
% data.test = 'yes'/'no'
% data.anonymise = 'yes'/'no'
% data.current_series_name = extension
% data.number_of_operations = (counts 1 per sort/convert);
% data.reco_option = 'Not Set' at start, then changed to
% data.total_number_of_files
% data.number_of_conversions_complete
% 'Reconstruct All Raw Scans'
% 'Reconstruct This Scan'
% 'Do not reconstruct'
% by questdlg in convert_to_analyze_func.m
% data.slice_reorder = 'yes'/'no'
% data.convert_to_3d = 'yes'/'no' - for recon data ('no' for multi-echo)
% data.conversion_time ; for timing processing
%
% Credits
% 1) Jimmy Shen's NIfTI toolbox
% http://www.mathworks.com/matlabcentral/fileexchange/8797
% 2) Stefano Gianoli : A lot of the GUI operation copied from renamefiles.m
% http://www.mathworks.com/matlabcentral/fileexchange/loadFile.do?objectI
% d=7077&objectType=file
%
%
% Bugs and shortcomings
% 3) Series title, scan number and image number are identified by their
% relation to a series of "."s in the .IMA name. Probably different for other scanners
% 4) Doesn't really provide orientation infomation in the analyze header.
% Strictly speaking this should all be done according to "Method 3"
% -http://nifti.nimh.nih.gov/pub/dist/src/niftilib/nifti1.h- using the
% hdr.hist.srow_* parameters
%
%
% Modifications
% v1.1 i) Repaired selection of output directory
% ii) Added log of the conversion
% iii) Included version numbering in logs and title
% v1.2 i) Included reconstruction of raw data (slice order and
% orientation needs fixing)
% ii) Fixed ui object handles (everything now refers to parent
% "obj")
% iii) Checks on write permissions for log and making directories in writefile directory
% iv) Changed behaviour with unknown sequence types. Now guesses
% matrix sizes and issues a warning
% v) Dumps dicominfo to same file as the text section of the dicom
% header (Gives TE, TR, operator name, coil etc)
% v1.3 i) Asymmetric fields of view and matrix sizes handled properly
% ii) Slice gap included in slice thickness if present
% iii) Voxel size calculation modified to work for 3D
% iv) Corrected slice order and rotation in reconstruction
% v1.4 i) Put getting of header parameters and putting these into the
% analyze header as two separate functions, get_header_parameters.m and
% make_analyze_header.m, which are called by the reco_raw_data_func as
% well, so reconstructed data has complete (well, better) header info
% ii) Introduced the scaling factors .hdr.dime.scl_inter and
% .hdr.dime.scl_slope
% iii) A less verbose log, except in test mode
% iv) Identification of sag, axial or cor (not currently used)
% v) Bug sorted. Until now a two-column shift was introduced in the NIfTI (but not analyze)
% option. Corrected.
% vi) More asymmetric matrix sizes / imaging orientations working.
% vii) Put conversion of a single image from mosaic and image
% rotation as a separate function - process_one_slice_func.m
% viii) Introduced a warning string which is displayed at the end if
% there were warnings
% ix) Modified start-up positioning on display - needed for
% laptops/small monitors
% v1.5 1) Replaced findstr (which searches for any match between str1 and
% str2) by strfind (which looks for str1 in str2) in
% write_dcm_text_header.m. Ellimated bogus finding of search strings
% 2) write_dcm_text_header.m replaced by write_dcm_text_header_with_guidata.m.
% It's not text header info, but it's too useful to leave
% unavailable to further programs. Orientation is now written into
% each text header.
% v1.6 1) Tidied up extraction of scan and image name via the
% data.NFullstopsPrior parameter. Works automatically with anonymised images (those exported as anonymised on export from the scanner) and should
% allow easier extension to other sites
% 2) Allows data to be reformatted after conversion with the
% reformat_data.m function, called in convert_to_analyze.m
% 3) Added a scan log, containing useful info about each scan (type,
% protocol name, parameters); write_scan_details. One-off info is
% written in convert_to_analyze.
% 4) Via a new checkbox, allows the user to select only to produce a scan list
% "scanlistonly".
% 5) Modified the progressbar so it doesn't pop up annoyingly
% with every new scan
% 6) Anonymises dicom images
% If data.anonymise is set to 'yes', as it now is by default, this removes
% the subject/Patient name from dicom headers, takes the name out of the
% text_header.txt, record of the original file name, and out of the scan
% list. The dicom header still full details of:
% Patient ID :
% Patient Date of Birth :
% Patient Sex :
% Patient Age :
% Patient Weight :
% Additional Patient History :
% Acquisition Date :
% Acquisition Time :
% Accession Number :
% Institution Name :
% Performing Physician's Name :
% Operator's Name :
% If you wish to remove these please use another anonymiser (such as
% the LONI De-identification Debablet -
% http://www.loni.ucla.edu/Software/Software_Detail.jsp?software_id=23)
% Given that this is an open-source WIP (in which data.anonymise can be set to 'no'
% for instance, the responsibility
% for ensuring that no subject/patient
% details are communicated to people not authorised to know these
% remains with the person sending images or taking them off site.
% v1.7 1) Sorted out reformatting of mosaic images with odd matrix sizes.
% An even number of pixels seems always to be assigned. Needs the
% isodd.m function
% 2) Sorted out the workbar (progress bar) again. But properly this
% time
% 3) The has been a problem with the originator in early versions of SPM (pre-SPM5), meaning that the originator was taken to be [256 0 0], and there was no overlap with SPM templates, so normalisation didn't work. Jimmy Shen has modified his "save_nii.m" so that a .mat file with the affine transform is written, and I have put the same mods in convert_to_analyze.m.
% v1.8 1) A new form of 'light' anonimisation introduced using dicomanon.
% v1.9 1) If NIfTI format is selected, the sorted data is written to a directory called 'nifti', not 'analyze'.
% v1.10 1) Bug fix of Anonymisation, so that it now does new-style 'light' (and slow) anon for MATLAB versions 2006b and above, old-style anon (whose DICOM output can't be interpreted correctly by Brain Voyager) for older MATLAB versions.
% 2) More possibilities for reformatting data, and more transparent in reformat_data_func.m (multi-echo, multi-channel, mag and phase)
% 3) Got rid of many of the get_ functions, replaced by a single get_dicom_fieldname_func.m
% 4) Introduced a data.features variable ('Basic'/'Advanced') to limit control some more fragile functions, and so I can modify
% the output (particular of multi-echo, multi-channel data with reformat_data) to suit development needs, without pissing people off
% 5) Introduced a 'data.user' parameter so I can tailor some function to users.
% 6) Moves all .IMA into a subdirectory as a final step, unless in test mode or no .IMA files present
% v1.11 1) Sorts into a directory named subjectID_accessionnumber
% 2) Moves sorted IMA to ima_to_delete at same directory level as subjectID_accessionnumber (fps of all
% files now closed properly), making it easy to find and delete the
% source data. To turn this off (e.g. for testing/debugging), change test from 'no' to 'yes' in
% dicom_sort_convert_main.m
% v1.12 1) Removed DICOM warnings
% 2) Added orientation and angle logging in scan list
% 3) Switched to using dicominfo.ProtocolName as label in scan_list.txt rather than tProtocolName[0]in
% text header, which has a tendency to get messed up
% 4) There is now a separate time reported for creating scan list,
% sorting and conversion which uses the new function
% secs2hms
% 5) pixel dimensions (hdr.dime.pixdim) corrected for reformatted
% data (multi-channel and/or multi-echo and/or phase&magnitude)
% 6) previously no introductory details were written into the scan log if dicom sorting only was done. These are now written by
% write_introductory_comments.m
% 7) reformatting of data with more than 3 dimensions (non-mosaic)
% and more than 4 dimensions (mosaic) using reformat_data_func.m
% thoroughly reworked
% v1.13 1) script call to dicom_sort_convert_main introduced - see
% example_dscm_call.m
% v1.14 1) reformats DTI data, treating number of gradient directions
% like repetitions in non-mosaic EPI
% v1.15 1) If the patient ID or accession number contain illegal characters, suggests alternative directory name
% 2) Improved reformatting of multi-channel data into [x][y][z][time][echos][channels][phase/mag] in the reformat directory, which works for 8, 24 and 32-element coils
% v1.17 1) Two-file NIfTI (.img/.hdr) method repaired
% 2) REPORT files are now moved to separate directory (report). There is one REPORT file per scan and they can be used to pheonix protocols
% 3) abbreviated scan parameters in the summary list (scan_list.txt)
% 4) made compatible with new VB17 file and dicom formats
% - removes leading zeros in directory name list (scan_names)
% - jumps over a new kind of DUMMY scan with dcminfo.SeriesDescription 'StartFMRI' in execute_sort_and_convert_Callback.m
% 5) writes a few obvious acquisition parameters for unknown sequence types
% 6) Fixed: a bug in the > 4D reformatting for interleaved sequences with an odd number of slices, that meant that the last odd slice was getting lost
% 7) Renamed buttons a bit to make it clearer what they do
% v1.18 1) In the test = 'no' mode, IMA data and REPORT files are zipped to ima.tar.gz. If data.delete_data_asat = 'yes', the original IMA data are deleted after tarring (--remove-files). If tarring and zipping fails for some reason, IMA data are moved to an ima_to_delete directory instead
% 2) Converting from mosaic format. If the mosaic image size does not tally with the read or phase matrix size, an attempt is made to identify the right matrix size
% If it crashes in this function (process_one_slice.m) it now writes which IMA file it was processing when it crash (so it's easier to check if this was corrupt)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%% Begin User-defined Parameters %%%%%%%%%%%%%%%%%%
% these choices are overwritten by data.* parameters in function calls to dicom_sort_convert_main
function data = set_data_defaults
data.anonymise = 'no';
data.test = 'no'; % no = move data to ima_to_delete directory after sort/convert, delete scan directories in list mode
data.define_writefile_subdir = 'yes';
data.version_number = '1.18';
data.readfile_filter = '*.IMA' ; %data.readfile_filter is set to this
switch ispc
case 1
data.default_startpath = 'C:\';
case 0
data.default_startpath = '/data';
end
data.features = 'Advanced'; %'Basic'/'Advanced'
% features = 'Advanced'; %'Basic'/'Advanced'
% data.user = 'Manuela'; %''/'Simon''Manuela',
data.user = 'Simon'; %''/'Simon''Manuela',
% Everyone can have their own most useful startpath, overrides general
% defaults here
switch data.user
case 'Simon'
data.default_startpath = 'F:\dicom_sort_test';
otherwise
end
data.log_style = 'normal';
data.readfile_dir = data.default_startpath;
data.writefile_dir_selected = data.default_startpath;
data.retain_dicom = 'no';
data.convert = 'yes';
data.convert_format = 'nifti';
data.current_conversion = '';
data.slice_reorder = 'yes';
data.scanlistonly = 'no';
data.write_an_extra_scanlist = 'no';
data.workbar_off = 'no';
data.delete_data_asat = 'yes'; % delete data After Sorting And Tarring
data.number_of_operations = 0;
warning off MATLAB:nonIntegerTruncatedInConversionToChar;
end
%%%%%%%%%%%%%%%%%%% End User-defined Parameters %%%%%%%%%%%%%%%%%%
if (nargin == 0)
clear data;
data = set_data_defaults;
data.gui = 1;
%%%%%%%%%%%%%%%%%%% GUI definition %%%%%%%%%%%%%%%%%%
grey_level=0.8;
set(0,'Units','pixels') ;
scnsize = get(0,'ScreenSize');
figure('MenuBar','none',...
'Name', ['Sort and/or Convert Siemens DICOM to NIfTI. v' data.version_number],...
'NumberTitle','off',...
'Position',[40,scnsize(4)-40-600,430,600],...
'CreateFcn', @figure_CreateFcn,...
'HandleVisibility','callback');
else
clear data;
data = set_data_defaults;
script_selections = varargin{:};
% overwrite all fields of 'data.' with selections in 'script_selections'
fieldnames_script_selections = fieldnames(script_selections);
for i=1:length(fieldnames_script_selections);
data.(fieldnames_script_selections{i})=script_selections.(fieldnames_script_selections{i});
end
data.gui = 0;
obj = 'no gui';
select_sort_and_convert_Callback(obj,data);
end
function figure_CreateFcn(obj, eventdata, handles)
% Construct the components
butt_select_us_dicom = uicontrol(obj,...
'Style','pushbutton',...
'String','Select IMA directory',...
'Position',[10,600-25-10,200,25],...
'Callback',{@select_us_dicom_Callback});
butt_select_destination = uicontrol(obj,...
'Style','pushbutton',...
'String','Select Destination directory',...
'Position',[10+200+10,600-25-10,200,25],...
'Callback',{@select_destination_Callback});
butt_sort_and_convert = uicontrol(obj,...
'Style','pushbutton',...
'String','GO!',...
'Position',[10,10,410,25],...
'Callback',{@select_sort_and_convert_Callback});
checkbox_convert = uicontrol(obj,...
'Style','CheckBox',...
'BackgroundColor', [grey_level grey_level grey_level],...
'String','Convert to',...
'Position',[10,600-70,90,25],...
'Callback',{@convert_Callback});
checkbox_retain_dicom = uicontrol(obj,...
'Style','CheckBox',...
'BackgroundColor', [grey_level grey_level grey_level],...
'String','Sort DICOMs into dirs and anonymise',...
'Position',[10,600-115,300,25],...
'Callback',{@dicom_retain_Callback});
checkbox_scanlistonly = uicontrol(obj,...
'Style','CheckBox',...
'BackgroundColor', [grey_level grey_level grey_level],...
'String','Only produce a list of scans',...
'Position',[10,600-140,250,25],...
'Callback',{@scanlistonly_Callback});
p = uibuttongroup('Position',[.25,.84,.3,.1],...
'BackgroundColor', [grey_level grey_level grey_level],...
'BorderType', 'none');
radiobutton_NIfTI = uicontrol('Style','RadioButton',...
'String','NIfTI (.nii)',...
'BackgroundColor', [grey_level grey_level grey_level],...
'Position',[10,30,150,20],...
'Parent',p);
radiobutton_analyze = uicontrol('Style','RadioButton',...
'String','two-file NIfTI (.img/.hdr pair)',...
'BackgroundColor', [grey_level grey_level grey_level],...
'Position',[10,10,220,20],...
'Parent',p);
splash_figure_filename = which('splash_figure.png');
splash_image = imread(splash_figure_filename);
splash_figure_pushbutton = uicontrol('style','pushbutton',...
'Position',[10,40,410,411],...
'CData',splash_image,...
'Enable','Inactive');
set(p,'SelectionChangeFcn',@radiobuttongroup_action);
set(p,'SelectedObject'); % Default is NIfTI
set(checkbox_convert,'Value',1);
guidata(obj,data);
function dicom_retain_Callback(obj,eventdata)
data = guidata(obj);
if (get(checkbox_retain_dicom,'Value') == get(checkbox_retain_dicom,'Max'))
data.retain_dicom = 'yes';
else
data.retain_dicom = 'no';
end
guidata(obj,data);
end
function scanlistonly_Callback(obj,eventdata)
data = guidata(obj);
if (get(checkbox_scanlistonly,'Value') == get(checkbox_scanlistonly,'Max'))
data.scanlistonly = 'yes';
data.convert = 'no';
data.retain_dicom = 'no';
data.current_conversion = '';
data.convert_format = '';
set(p,'SelectedObject',[]);
set(checkbox_convert,'Value',0);
set(checkbox_retain_dicom,'Value',0);
set(checkbox_retain_dicom,'Enable','off');
set(checkbox_convert,'Enable','off');
set(radiobutton_NIfTI,'Enable','off');
set(radiobutton_analyze,'Enable','off');
else
data.scanlistonly = 'no';
set(checkbox_retain_dicom,'Enable','on');
set(checkbox_convert,'Enable','on');
set(radiobutton_NIfTI,'Enable','on');
set(radiobutton_analyze,'Enable','on');
convert_Callback(obj,eventdata);
dicom_retain_Callback(obj,eventdata);
end
guidata(obj,data);
end
function convert_Callback(obj,eventdata)
data = guidata(obj);
data.scanlistonly = 'no';
get(checkbox_convert,'Value');
if (get(checkbox_convert,'Value') == get(checkbox_convert,'Max'))
data.convert = 'yes';
data.convert_format = 'nifti';
set(p,'SelectedObject',radiobutton_NIfTI); % Select NIfTI first
else
data.convert = 'no';
data.convert_format = '';
set(p,'SelectedObject',[]); % Deselect both
end
guidata(obj,data);
end
function radiobuttongroup_action(obj,eventdata)
data = guidata(obj);
format_select_string = (get(get(obj,'SelectedObject'),'String'));
if findstr(format_select_string, 'two-file NIfTI (.img/.hdr pair)')
data.convert_format = 'analyze';
elseif findstr(format_select_string, 'NIfTI (.nii)')
data.convert_format = 'nifti';
else
data.convert_format = 'Analyze Format Not Attributed';
end
guidata(obj,data);
end
end
function select_us_dicom_Callback(obj,eventdata)
data = guidata(obj);
readfile_dir = uigetdir(data.readfile_dir);
if ~isnumeric(readfile_dir)
data.readfile_dir = readfile_dir;
data.writefile_dir_selected = readfile_dir;
guidata(obj,data);
end
end
function select_destination_Callback(obj,eventdata)
data = guidata(obj);
writefile_dir_selected = uigetdir(data.writefile_dir_selected);
if ~isnumeric(writefile_dir_selected)
data.writefile_dir_selected = writefile_dir_selected;
guidata(obj,data);
end
end
end
