5.2.0

.gitignore

@@ -1,6 +1,11 @@
 # Ignore Mac DS_Store files
 .DS_Store
 
+# Ignore file with private information
+imlook4d-zip-and-release-to-google-drive
+release to google drive/client_secrets.json
+release to google drive/mycreds.txt
+
 # Ignore MATLAB backup files
 *~
 

TODO.txt

@@ -6,8 +6,8 @@ ERRORS
 [  ]   Help on Buttons TACT, Clear.  Help on drop down "Clear ROI"
 [  ]   Command Button('TACT') does not work. Button('Clear') works.
 [  ]   Help now goes all the way up to "Image View Port".  Rewrite so it goes only to parent
-[  ]   Help on Record button missing
-
+[  ]   Help on Record button missing  
+ 
 
 
 

imlook4d/DOCS/Models_exported_to_html/.~lock.Models.html#

@@ -0,0 +1 @@
+,jan,Linux,25.06.2020 11:51,file:///mnt/Data/home/jan/.config/libreoffice/4;

imlook4d/HELP/Export times to sif.txt

@@ -0,0 +1,13 @@
+<h1>Export times to sif</h1>
+<HR></HR>
+<!------------------->
+
+	<P>
+	Nifti files do not carry information about time, which is necessary in some processing of dynamic scans.
+    This script exports time information from a DICOM file to a .sif file.
+	</P>
+
+
+	<P>
+	Nifti files can obtain time information by importing it from a .sif file. See "Import times from sif"
+	</P>

imlook4d/HELP/Import times from sif.txt

@@ -0,0 +1,17 @@
+<h1>Import times from sif</h1>
+<HR></HR>
+<!------------------->
+
+	<P>
+	Nifti files do not carry information about time, which is necessary in some processing of dynamic scans.
+    This script import time information from a .sif file.
+	</P>
+
+
+
+
+	<P>
+	.sif files can be created from the original DICOM files (which carry time information), by "SCRIPTS/Matrix/Export times to sif"
+
+	</P>
+

imlook4d/HELP/Open.txt

@@ -9,6 +9,7 @@
 			<LI> <B><a href="javascript:;" onclick="document.location.hash='ROI';">ROI file + image </a> </B> (.roi)
 			<LI> <B><a href="javascript:;" onclick="document.location.hash='DICOM';">DICOM</a> </B>
 			<LI>  <B><a href="javascript:;" onclick="document.location.hash='Nifti';">Nifti</a> </B> (.nii, .hdr, .img)
+			<LI>  <B><a href="javascript:;" onclick="document.location.hash='Nifti-pmod';">Nifti PMOD</a> </B> (.nii)
 
 			<LI>  <B><a href="javascript:;" onclick="document.location.hash='ECAT';">Siemens/CTI ECAT 7</a></B> (.v)
 			<LI>  <B><a href="javascript:;" onclick="document.location.hash='Analyze';">Analyze</a> </B> (.hdr, .img)
@@ -110,6 +111,20 @@
 	</P>
 
 
+<a href="javascript:;" onclick="document.location.hash='top';">[top]</a>
+
+<h2><a id="Nifti-pmod">Nifti file opening (PMOD)</a></h2>
+<!------------------------>
+
+	<P>
+		Opens  .nii files (one binary file), converted from Dicom using PMOD. This is read-only. 
+	</P>
+
+	<P>
+		Time information from 4D PET is imported using the PMOD Nifti extension format.
+	</P>
+
+
 <a href="javascript:;" onclick="document.location.hash='top';">[top]</a>
 <h2><a id="ECAT">Siemens ECAT file opening</a></h2>
 <!------------------------>

imlook4d/HELP/SPM Tissue probability map ROIs.txt

@@ -2,7 +2,7 @@
 <HR></HR>
 <!------------------->
 	<P>
-		Finds the following region-of-interests (ROIs) from the tissue-probability maps for this file:
+		Finds the following region-of-interests (ROIs), calculated from the tissue-probability maps for this file:
 <ol>
 <li> Gray Matter
 <li> White Matter
@@ -14,10 +14,6 @@
 </ol>
 	</P>
 
-	<P> 
-Nifti cannot store ROI names. ROI names may be loaded using the script "ROI/ROI naming from file", where "TPM_Based_ROIs.txt" should be selected.
-	</P>
-
 	<P> 
 
  This script uses files named c1xxx to c5xxx that are created prior to this script, when the user executed "Apply atlas". 

imlook4d/HELP/align.txt

@@ -14,8 +14,12 @@
 	</P>
 
 	<P> 
-        The alignment reads a 4D nifti file and uses the spm spatial realignment functions. 
+        The alignment reads a 4D nifti file and uses the spm spatial realignment functions optimized for PET. 
 	</P>
 
+	<P> 
+        For PET, often the first frames are meaningless being only noise.  This may cause the realignment to fail.  Therefore, you will in a dialog need to
+        define the first frame to use for realignment.  
+	</P>
 	<P> 
 	</P>

imlook4d/HELP/transparancyEdit.txt

@@ -0,0 +1,11 @@
+<h1>Transparancy Edit</h1>
+<HR></HR>
+<!------------------->
+	<P>
+	This value between 0-100 % sets the weight of the frontmost image.  A lower value shows more of the underlying image.
+	</P>
+
+
+	<P>
+	This setting is shown only if overlay images are shown.
+	</P>

imlook4d/SCRIPTS/Change/Duplicate.m

@@ -124,13 +124,17 @@
        set( HmatchNew(i), 'String',  get( HmatchOld(i), 'String') );
     end
 
+    % Copy status of transparancyPanel
+    newHandles.transparancyPanel.Visible = imlook4d_current_handles.transparancyPanel.Visible;
+    newHandles.transparancyText.Visible = imlook4d_current_handles.transparancyText.Visible;
+    newHandles.transparancyEdit.Visible = imlook4d_current_handles.transparancyEdit.Visible;
+
     % Copy record-button status
     tag = 'record_toolbar_button';
     HmatchOld = findobj(imlook4d_current_handle,'Tag',tag);
     HmatchNew = findobj(newHandle,'Tag',tag);
     set( HmatchNew(1), 'State',  get( HmatchOld(1), 'State') );
 
-
  %   
  % FINALIZE
  %     

imlook4d/SCRIPTS/Matrix/Export_times_to_sif.m

@@ -0,0 +1,51 @@
+StoreVariables
+Export
+
+
+
+timeScale = imlook4d_time';
+duration = imlook4d_duration';
+activity = zeros( size(imlook4d_time))';
+
+
+[file,path] = uiputfile( {...
+    '*.sif', 'Turku (blood/weight)  (*.sif)' ...
+    }, ...
+    'Export times to sif file', 'TACT.sif');
+
+[pathstr,name,ext] = fileparts(file);  % To get extension
+fullPath=[path file];
+
+%
+% Copied from SaveTact.m
+%
+
+    % Simplified sif file, from one ROI
+
+
+    % Header info
+    scan_start_time = 'xx/xx/xxxx xx:xx:xx'
+    number_of_frames = length(imlook4d_time);
+    number_of_columns = 2 + size(activity,2) ;
+    SIF_version = '1';
+    study_ID = 'xxxx';
+    isotope = 'X-XX';
+
+    if (  size(activity,2) == 1 )
+        activity = [ activity activity ];  % Sif seems to require 4 columns (minimum)
+        number_of_columns = 2 + size(activity,2) ;
+    end
+
+    tactHeader=[sprintf(['%s' '\t'], scan_start_time, num2str(number_of_frames), num2str(number_of_columns), SIF_version, study_ID, isotope) ];
+    tactHeader=tactHeader(1:end-1); % Remove last TAB
+
+    unitFactor = 1; % Do nothing
+    try
+
+        save_cellarray( num2cell([ timeScale (timeScale+duration) unitFactor*double(activity) ]), fullPath, tactHeader );
+    catch
+        %disp('You selected not to save TACT curve');
+    end
+
+Import
+%ClearVariables

imlook4d/SCRIPTS/Matrix/sort.txt

@@ -23,5 +23,7 @@ Exchange_Slices_to_Frames.m
 ---
 #Additional_:
 Import_times_from_sif.m
+Export_times_to_sif.m
+---
 Matrix_to_ROI.m
 ScreePlot.m

imlook4d/SCRIPTS/SPM/SPM_Tissue_probability_map_ROIs.m

@@ -14,6 +14,18 @@
 if ~verifySpmExists()
     return
 end
+
+Export;
+
+currentFile = imlook4d_current_handles.image.file;
+
+if (startsWith(currentFile,'mni') )
+    warndlg({'Tissue probability map ROIs must be calculated from native-space image'})
+    return
+end
+
+
+
 StartScript; % Start a script and open a new instance of imlook4d to play with
 
 % Data fields that can be modified in your own code:
@@ -32,10 +44,15 @@
 
 %% Open c1-c5
 
-currentFile = imlook4d_current_handles.image.file;
-cFile = [ 'c1' currentFile];
+oldDir = pwd();
+cd( imlook4d_current_handles.image.folder);
 
 % Open c1
+cFile = [ 'c1' currentFile];
+if ~isfile( cFile )  % Correct file name, may have used 'mean' for a dynamic scan
+    cFile = strrep( cFile, 'c1', 'c1mean')
+end
+
 V = spm_vol(cFile);
 A = spm_read_vols(V); % Individual's c1... file
 
@@ -49,6 +66,11 @@
 % Open c2-c5
 for i = 2:5
     cFile = [ 'c' num2str(i) currentFile];
+    if ~isfile(cFile)  % Correct file name, may have used 'mean' for a dynamic scan
+        was = ['c' num2str(i)]; % 'c2'
+        is = [was 'mean']; % 'c2mean'
+        cFile = strrep( cFile, was, is);
+    end
     V = spm_vol(cFile);
     A = spm_read_vols(V); % Individual's c1... file
     M(:,:,:,i) = A;
@@ -76,11 +98,13 @@
 V = spm_write_vol(V, NewROIs);
 
 LoadROI(newFile);
-
+ROI_naming_from_file( which( 'TPM_based_ROIs.txt'));
+copyfile( which( 'TPM_based_ROIs.txt'),  pwd() ); % is in target directory (cd at top of file)
 
 % --------------------------------------------------
 % END OF OWN CODE
 % --------------------------------------------------
+cd(oldDir);
 
 %EndScript; % Import your changes into new instance and clean up your variables
 

imlook4d/SCRIPTS/SPM/align.m

@@ -32,19 +32,34 @@
 % START OWN CODE:
 % --------------------------------------------------
 
+
+% First frame dialog
+prompt={'First frame (noisy data does not align)'};
+[answer, imlook4d_current_handles] = ModelDialog( imlook4d_current_handles, ...
+    'align', ...
+    prompt, ...
+    { '1' } ...
+    );
+
+firstFrame = str2num(answer{1});
+
+% Setup realignment
+
 spm('defaults','pet');
 spm_jobman('initcfg');
 
 matlabbatch{1}.spm.util.exp_frames.files = { [path ',1']};
 %matlabbatch{1}.spm.util.exp_frames.files = {'/Users/jan/Desktop/IMAGES/DAD-tests/D34/native/Sharp.nii,1'};
-matlabbatch{1}.spm.util.exp_frames.frames = [1 : numberOfFrames];
-%matlabbatch{1}.spm.util.exp_frames.frames = [1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18];
+
+
+matlabbatch{1}.spm.util.exp_frames.frames = [firstFrame : numberOfFrames];
+disp( ['Aligning frames = ' num2str(firstFrame) ' - ' num2str(numberOfFrames ) ]);
 
 matlabbatch{2}.spm.spatial.realign.estwrite.data{1}(1) = cfg_dep('Expand image frames: Expanded filename list.', substruct('.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));
 matlabbatch{2}.spm.spatial.realign.estwrite.eoptions.quality = 0.9;
 matlabbatch{2}.spm.spatial.realign.estwrite.eoptions.sep = 4;
 matlabbatch{2}.spm.spatial.realign.estwrite.eoptions.fwhm = 5;
-matlabbatch{2}.spm.spatial.realign.estwrite.eoptions.rtm = 1;
+matlabbatch{2}.spm.spatial.realign.estwrite.eoptions.rtm = 1; % Register to mean
 matlabbatch{2}.spm.spatial.realign.estwrite.eoptions.interp = 2;
 matlabbatch{2}.spm.spatial.realign.estwrite.eoptions.wrap = [0 0 0];
 matlabbatch{2}.spm.spatial.realign.estwrite.eoptions.weight = '';

imlook4d/SCRIPTS/SPM/atlas_GM.m

@@ -38,6 +38,12 @@
 
 GM_ROI_file = [ folder filesep 'c1' FILE ext];
 
+% Dynamic files has been using mean file, fix name
+if ~isfile(GM_ROI_file)
+    disp('assuming mean file')
+    GM_ROI_file = strrep( GM_ROI_file, 'c1', 'c1mean')
+end
+
 try
     nii = load_nii(GM_ROI_file);
     openingMode='load_nii';

imlook4d/SCRIPTS/View/Background_image__add.m

@@ -70,4 +70,10 @@
 end
 %end
 
+% Show transparancy setting
+imlook4d_current_handles.transparancyEdit.Visible = 'on';
+imlook4d_current_handles.transparancyText.Visible = 'on';
+imlook4d_current_handles.transparancyPanel.Visible = 'on'; 
+
+% Finish
 ClearVariables

imlook4d/SCRIPTS/View/Background_image__remove.m

@@ -5,6 +5,14 @@
 imlook4d_current_handles.image.backgroundImageHandle = [];
 imlook4d_current_handles.image.CachedImage2 = [];
 Import
+
+
+% Show transparancy setting
+imlook4d_current_handles.transparancyEdit.Visible = 'off';
+imlook4d_current_handles.transparancyText.Visible = 'off';
+imlook4d_current_handles.transparancyPanel.Visible = 'off'; 
+
+% Finish
 ClearVariables
 
 clear imlook4d_current_handles.image.backgroundImageHandle

imlook4d/external functions/loop/loop.m

@@ -49,6 +49,7 @@
 
     disp('=================================');
     disp(['DATA SOURCE (for loop)' ]);
+    disp(['   Time        = ' char(datetime()) ]);
     disp(['   Function    = ' functionName ]);
     disp(['   Excel file  = ' xlsFileList ]);
     disp(['   Excel sheet = ' sheet ]);
@@ -165,7 +166,7 @@
                     '   NOTE : Found ' num2str(emptyColumns) ' empty fields' ]);
 
                 % Create emtpy table row
-                T2 = cell2table( num2cell(nan(1,17)) );
+                T2 = cell2table( num2cell(nan(1,size(T,2))) );
                 T2.Properties.VariableNames = T.Properties.VariableNames;
 
                 for i = 1 : size(T,2)