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% .
%
% #yk ANTx2
%
% #b ⇒ Respository: <a href= "https://github.com/ChariteExpMri/antx2">GitHub:github.com/ChariteExpMri/antx2</a>
% #b ⇒ Tutorials: <a href= "https://chariteexpmri.github.io/antxdoc/">https://chariteexpmri.github.io/antxdoc/</a>
% #b ⇒ Templates : <a href= "https://drive.google.com/drive/folders/1q5XOOVLvUYLqYsQJLqNRF7OK8fNwYhI9">googleDrive:animal templates</a>
%
%
%======= CHANGES ================================
% #ra 07 May 2019 (14:16:48)
% #ok new version "ANTx2"
% - SPM-package: SPM12
% - templates were outsourced and can be downloaded from:
% https://drive.google.com/drive/u/1/folders/1q5XOOVLvUYLqYsQJLqNRF7OK8fNwYhI9
% - linux/mac/windows
% #ra 08 May 2019 (01:34:19)
% addedd icon panel [iconpannel4spm.m] for manual preregistration step to facilitate manual
% registration step
% #ra 22 May 2019 (12:19:03)
% addded: [xcoregmanu.m] - manually coregister images
% #ra 07 Aug 2019 (14:23:20)
% initial rigid registration (xwarp3) modified for more robust registration
% [checkRegist.m]: GUI to check registration of several images
% [getorientation.m]: GUI to examine the apriory orientation (how animal is positioned in scanner)
% - run it without input arguments or use context menu from ANT animal listbox
% - the respective ID/number of orientation can be used to define the "orientType" in the projectfile
% #ra 16 Oct 2019 (03:42:04)
% 1)"create study templates"-step can be performed before running the normalization step
% ..see Main/Create Study Templates
% 2)two new "get-orientation"-functions implemented. Functions can be used if the orientation of
% the native image (t2.nii) is unknown. See animal listbox context menu
% (2a) "examineOrientation" #k [getorientation.m] #n using apriori rotations,..
% best orientation selected via eyeballing
% (2b) "getOrientationVia3points" #k [manuorient3points.m] #n using 3 manually tagged corresponding points in
% source and reference image
% --> 2b approach is easier and faster for difficult rotations
% function modifications: uhelp, plog
% #ra 17 Oct 2019 (22:04:14)
% [xregisterCT/CTgetbrain_approach2]: added parameter "bonebrainvolume" for more robust cluster-identifaction
% #ra 29 Oct 2019 (23:28:16)
% modif. files [cfg_getfile2], [uhelp]
% #ra 04 Nov 2019 (11:35:28)
% set up GITHUB repository #bw https://github.com/ChariteExpMri/antx2/
% -primary checks macOS, Linux MINT
% -updated [uhelp]
% #ra 13 Nov 2019 (00:47:38)
% [maskgenerator] added region-lection list and online link to compare selected regions
% #ra 15 Nov 2019 (02:14:16)
% [maskgenerator] added "find" region-panel
% #ra 22 Nov 2019 (11:37:49)
% [maskgenerator] added alpha-transparency slider and display number-of-rows pull down
% checked regions of new Allen2017Hikishima template
% #ra 11 Dec 2019 (14:41:37)
% [xcoreg] fix filename bug; display missing files
% [uhelp]: allows column-wise/selectionwise copying
% #ra 07 Jan 2020 (15:40:52)
% matlab19b fix: cfg_getfiles2: data from server
% sub_atlaslabel2xls: added writetable if xlwrite not working (matlab2017 upwards issue)
% #ra 27 Jan 2020 (09:43:48)
% [xexcel2atlas.m]: create atlas from excelfile, excelfile is a modified version of the ANO.xlsx
% [sub_write2excel_nopc]: subfun: write excel file for mac/linux
% #ra 28 Jan 2020 (10:14:11)
% [xexcel2atlas.m]: added information
% #ra 31 Jan 2020 (14:07:48):
% [xgetlabels4]: allowing readout from "other Space"
% #ra 04 Feb 2020 (18:03:15)
% rat-brain segmentation accelerated
% #ra 17 Feb 2020 (12:32:00)
% set-up pipeline for etruscian shrew
% [xcoreg]: enables elastix registration with multiple paramter files (regid&|affine&|bspline) and
% without spm-registration, (set "task" to [100])
% #ra 19 Feb 2020 (15:15:55)
% [xdraw.m]: manual drawing tool to create masks ->>Tools/"draw mask"
% #ra 09 Mar 2020 (12:31:52)
% etrucian-shrew modified templates --> not finalized jet
% [approach_60] t2.nii to "sample"-registration: register t2.nii to another t2.nii-sample in standard space
% Par0033bspline_EM3.txt: bspline-paramter file works well with "sample"-registration
% #ra 11 Mar 2020 (17:28:49)
% [xsegmenttube]: segment several animals from the same image /tube
% [xsplittubedata]: split data-sets based on tube-segementation
% #ra 20 Mar 2020 (12:30:38)
% [case-filematrix]: export selected files from selected folders
% #ra 14 May 2020 (14:14:07)
% [elastix_checkinstallation] addeed (extras/troubleshoot) .. fct to check installation of elastix-program
% [uhelp.m] modified: selection color
% [checkRegist] modified: changed image2clipboard function
% [summary_export] added (available via context menu of "PR"-radio in ANT-main window)
% .. export HTML-summary (ini/coreg/segm/warp) structure to exporting folder
% #ra 15 May 2020 (17:33:52)
% [setup_elastixlinux.m] modified-->solved problem: stucked installation of MRICRON
% #ra 29 May 2020 (14:45:41)
% [xstatlabels] bugfixed
% [uhelp] added finder panel
% #ra 23 Jun 2020 (17:01:21)
% [doelastix.m] update, backward transformation now possible with userdefined voxel or dim-size
% #ra 23 Jun 2020 (17:13:43)
% 3D-volume visualization added (main menu .. grahics/3D-volume): allows to 3D-visualize atlas regions,
% nodes & links (connections/~strength) and statistical images/intensity images [xvol3d.m]
% -main features can be accessed via command line
% #ra 30 Jun 2020 (23:15:45)
% [xvol3d.m] -updated, tested Linux/MAX/WIN, added more options and label properties
% #ra 08 Jul 2020 (13:37:00)
% [dtistat]: revised; for DTI-connectivities allows input data from MRtrix; new command line access;
% new COIfile;
% #ra 03 Aug 2020 (12:50:16)
% debug Matlab19b error [xbruker2nifti].. in preadfile2: error occured due to uncommented code
% after 'return' command (varargin issue)
% #ra 04 Aug 2020 (16:38:17)
% [installfromgithub] small changes
% #ra 05 Aug 2020 (22:10:09)
% solved issue: unintended interaction between help window (mouse-over main menu) and ant-history window
% #ra 07 Aug 2020 (14:43:11)
% [xheadman.m] explicit output filename, added tooltips
% [skullstrip_pcnn3d]: added errorMSG if vox-size is to large
% [displaykey2.m]: bugfix with zooming
% #ra 07 Aug 2020 (17:36:56)
% [doelastix] (deform volumes elastix) now possible, apply registration-trafo to 4D-data (example: BOLD-timeseries) (..not parallelized yet)
% #ra 10 Aug 2020 (11:34:58)
% [doelastix] (deform volumes elastix) parallelized for 4D-data
% #ra 14 Aug 2020 (12:57:03)
% [getReferencePath] modified (layout with listbox, instead of buttons); recursive search for 'AVGT.nii' in (sub)/folder of ant-templates
% --> to overcome the (sub)/folder nestings in the ant-templates folder
% #ra 17 Aug 2020 (16:49:32)
% [paramgui] new version, (multi-icon style, execution-history)
% ..the old version is still available (via menu/preferences)
%
% [installfromgithub] BUG-solved: after 'rebuilding'...gui could not close and workdir did not go prev. study path
% #ra 24 Aug 2020 (09:27:02)
% new tutorial #bw ["tutorial_orientation_and_manucoreg.doc"]
% This tutorial deals with image orientation for template registration and manual coregistration.
% #gw --> access via ANT-menu: Extras/documentations or ..\antx2\mritools\ant\docs
% #ra 24 Aug 2020 (12:08:22)
% - getanatomicallabels [sub_atlaslabel2xls.m]: fixed bug.. writing excel table (mac) because newer cell2table-version
% variable names must match with Matlab variable style. This happens when animal names (such as "20130422_TF_001_m1_s3_e6_p1")
% start with a numeric value instead of a character). SOLUTION: In such cases animals the animals in the excel table
% will be renamed (adding a prefix 's' such as "s20130422_TF_001_m1_s3_e6_p1").
% #ra 27 Aug 2020 (15:42:11)
% [xvol3d_convertscores]: new function for xvol3d...allows to 3d colorize user-specific regions by scores/values (percentages/statist scores)
% #ra 28 Aug 2020 (10:43:27)
% - [uhelp] bug-fix: help-fig failed to update fontsize and fig-position after reopening
% - updates/changes ([antver.m]) can be inspected from the GITHUB webside.
% #ra 01 Sep 2020 (12:49:32)
% manual coregistration [displaykey3inv.m]: update help
% #ra 07 Sep 2020 (03:41:16)
% [xdownloadtemplate] DOWNLOAD TEMPLATES VIA GUI (faster alternative compared to webside).
% #gw --> Access via Extras/donwload templates --> unresolved/untested: proxy settings
% #ra 14 Sep 2020 (13:14:15)
% [xdownloadtemplate] DOWNLOAD TEMPLATES VIA GUI ..modified using curl (MAC/Linux) and wget.exe (windows)
% - Function was tested with and without proxies using Win, MAC & Linux
% #ra 17 Sep 2020 (13:45:38)
% [xgetlabels4] BUG solved: "zeros" in resulting excelFile
% #ra 21 Sep 2020 (12:46:16)
% [xsegmenttubeManu] added. This function allows to manually segment a Nifti-image containing several
% animals ("multi-tube" image). This function works as manual pendant to [xsegmenttube].
% #ra 22 Sep 2020 (00:14:08)
% [xdicom2nifti]: revised (now allows conversion using MRICRON or SPM)...Mac/Linux/WIN
% #ra 22 Sep 2020 (13:30:09)
% new tutorial #bw ['tutorial_convertDICOMs.doc']
% This tutorial deals with the conversion of dicom to NIFTI files.
% #gw --> access via ANT-menu: Extras/documentations or ..\antx2\mritools\ant\docs
% #ra 06 Oct 2020 (03:45:46)
% [xdraw] draw a (multi-) mask manually , improved version, allows otsu-segmentation, new image drawing
% tools, calculate volume for each mask-region, save as mask or save masked background image
% #gw --> access via ANT-menu: Tools/draw mask
% #ra 07 Oct 2020 (12:56:31)
% -[xdraw] : debug, added measuring tool (distance in mm/pixel and angle)
% #ra 13 Oct 2020 (10:46:14)
% - EXVIVO APPROACH: coregistration approach for splitted multi-tube skullstripped (exvivo) animals.
% The problem is the high intensity of the preserving substance enclosing the animal's brain.
% This resulted in a defective brain mask with subsequent suboptimal rigid registration.
% Solution: In the settings menu (gearwheel icon) set [usePriorskullstrip] to [4] and set the parameter
% file for rigid transformation [orientelxParamfile] to "..mypath\..\trafoeuler5_MutualInfo.txt"
% This has two effects: First, background intensity is removed and a peudo-mask of 't2.nii' ("_msk.nii")
% is created. Second, mutual information is used as metric for rigid transformation.
%
% - PARAMTER SETTING [antconfig] (gear wheel icon) has finally obtained a help window.
% #gw --> Access: When creating a new project (Menu: Main/new project) or selecting the [gear wheel icon]
% obtain the help window via bulb-icon (lower left corner of the paramter file)
% #ra 14 Oct 2020 (02:03:47)
% - [xdraw] drawing mask tool now includes a 3D-otsu segmentation
% #ra 14 Oct 2020 (17:53:20)
% - [xdraw] drawing mask tool: added contours and contour-based segmentation, completed help
% #ra 25 Oct 2020 (21:33:14)
% [xdraw] drawing mask tool: refurbished, containing tools:
% - advanced saving options,
% - contour line segmentation
% - ROI manipulation (translate/rotate/flip/copy/replace)
% - TODO: test MAC & LINUX : DONE!
% #ra 30 Oct 2020 (14:50:30)
% [SIGMA RAT template] (Barrière et al., 2019) added to gdrive
% - Paper : https://rdcu.be/b9tKX or https://doi.org/10.1038/s41467-019-13575-7
% - #gw --> access via link : https://drive.google.com/drive/u/2/folders/1q5XOOVLvUYLqYsQJLqNRF7OK8fNwYhI9
% or ANT menu: EXTRAS/download templates
% #ra 16 Nov 2020 (01:37:17)
% [atlasviewer.m] added. This function allows to display an atlas (NIFTI file) for example the
% 'ANO.nii' -file
% #gw --> access: ANT-MENU: Graphics/Atlas viewer
% -TODO: test MAC & LINUX : DONE!
% #ra 18 Nov 2020 (13:30:53)
% - [xdownloadtemplate.m] added: check internet connection status
% - new tutorial #bw ['tutorial_brukerImport.doc']
% This tutorial deals with conversion of Bruker data to NIFTI files.
% #gw --> access via ANT-menu: Extras/documentations or ..\antx2\mritools\ant\docs
% #ra 23 Nov 2020 (15:32:33)
% - [xrename]: extended functionality: now allows basic math operations of images such as
% ROI extraction, image thresholding, combine images (mask an image by another image)
% - other options of [xrename]: scale image, change voxel resolution (see help of xrename)
% #gw --> access via ANT-menu: Tools/manipulate files
% #ra 24 Nov 2020 (14:08:48)
% - NEW TUTORIAL #bw ['tutorial_prepareforFSL.doc']
% PROBLEM: How to use the backtransformed template brain mask for resting-state
% data processed via FSL. IMPORTANT..this tutorial is not finished!
% This tutorial explains the following steps
% 1. Set ANT path, make study folder +start ANT GUI
% 2. Download template
% 3. Define a project
% 4. Import Bruker data
% 5. Import templates for this study
% 6. Create a t2.nii image
% 7. Examine Orientation
% 8. Register t2.nii to the template
% 9. Back-transform template brain mask to native space
% 10. Extract 1st image of the 4D BOLD series
% 11. Coregister t2.nii onto BOLD (RS-) Data
% 12. Mask first EPI-image with brain mask
% 13. Scale up 4D data for FSL
% #gw --> access via ANT-menu: Extras/documentations or ..\antx2\mritools\ant\docs
% - NEW TUTORIAL #bw ['tutor_multitube_manualSegment.doc']
% PROBLEM: Several animals located in one image (I call this "multitube")
% This tutorial explains the following steps:
% 1. Manual segment images --> draw masks
% 2. Split datasets using the multitube masks
% #gw --> access via ANT-menu: Extras/documentations or ..\antx2\mritools\ant\docs
%
% #ra 16 Feb 2021 (15:46:57)
% - DTI-statistic and 2d-matrix/3d-volume visualization was extended
% functions: [dtistat.m], [xvol3d.m] and [sub_plotconnections.m]
% - get anatomical labels [xgetlabels4.m]: The paramter volume percent brain ("volpercbrain") was
% re-introduced in the resulting Excel-table
%
% #ra 13 Apr 2021 (21:52:21)
% - CAT-atlas (Stolzberg et al., 2017) added to google-drive
% #gw --> access via link : https://drive.google.com/drive/u/1/folders/1q5XOOVLvUYLqYsQJLqNRF7OK8fNwYhI9
% paper: https://onlinelibrary.wiley.com/doi/abs/10.1002/cne.24271
%
%
% #ra 06 May 2021 (10:29:16)
% fixed BUG in "rsavenii.m" (issue only for writing 4D-data only)
% #ra 07 May 2021 (22:15:55)
% -->started [checkreghtml]: make html-page of overlay of arbitrary pairs of images for selected animals
% #ra 10 May 2021 (20:39:32)
% #k [xcheckreghtml.m] #n implemented. This function create HTML-files with overlays of arbitrary images.
% The HTML-files can be used to check the registration, can be zipped and send to others.
% #gw --> access via ANT-menu: Graphics/generate HTML-file
%
% #ra 29 May 2021 (01:20:40)
% #k [xrealign.m] #n --> realign 3D-(time)-series or 4D volume using SPM-realign function
% #gw --> access via ANT-menu: Tools/realign images (SPM, monomodal)
%
% #ra 25 Jun 2021 (12:05:36)
% #k [xrealign_elastix.m]: #n multimodal realignment of 4D data (timeseries) using ELASTX and mutual information
% #gw --> access via ANT-menu: Tools/realign images (ELASTIX, multimodal)
%
% #ra 28 Jun 2021 (15:36:53)
% #k [show4d.m]: #n SHOW 4D-VOLUME / check quality of realignment of 4D-volume
% function allows to display a 4D-volume and it's realigned version side-by-side
% For quality assessment, the 1st volume is displayed on top (as contour plot) of the selected (3D)-volume
% #gw --> access via ANT-menu: Graphics/check 4D-volume (realignment)
%
% #ra 12 Aug 2021 (18:49:17)
% #k [xcheckreghtml.m] #n ... fixed BUG: "dimension"-parameter error with string/double vartype
% [checkpath] checks whether paths-names of ANTx-TBX, a study-project/template and data-sets contain special characters
% Special characters might result in errors & crashes.
% #gw --> access via ANT-menu: Extras/troubleshoot/check path-names
%
% #ra 16 Aug 2021 (11:18:29)
% #k [case-filematrix] #n add file functionality: copy/delete/export files ; file information
% #gw --> access via ANT-menu: Graphics/show case-file-matrix
% #ra 16 Aug 2021 (13:35:35)
% test: gitHub with "personal access token" : upload-seems to work/chk(TunnelBlick)
%
% #ra 18 Aug 2021 (12:24:04)
% #k [xrename.m]: #n added context menu for easier file manipulation (copying/renaming/expansion/deletion)
% and additional file information (file paths; existence of files; header information)
%
% #ra 19 Aug 2021 (21:02:37)
% #k [xstat.m]: #n added pulldown to select the statistical method to treat the multiple comparison problem
% #ba 19 Aug 2021 (23:50:18)
% #k [xrename.m]: #n now allows to threshold an image
% #gw --> access via ANT-menu: Tools/manipulate files
% #ba 23 Aug 2021 (14:12:17)
% #k [xcalcSNRimage.m] #n convert image to SNR-image
% according to Gudbjartsson H, Patz S. 1995: The Rician distribution of noisy MRI data. Magn Reson Med.; 34(6): 910914.)
% -can be used for Fluorine-19 (19F)-contrast images
% #gw --> access via ANT-menu: SNIPS/convert image to SNR-image
% #ba 08 Sep 2021 (10:42:24)
% #k [sub_sting.m] #n creates node-related needles with numeric annotations (labels) onto 3D-brain (for DTI-data)
% -annotations are view-dependent and will be adjusted accordingly
% -labels appear at positions along a circle circumventing the brain
% -labels can be manually repositioned
% -function is part of xvol3d.m/sub_plotconnections to display DTI-connection onto a 3D brain
%
% #ba 13 Sep 2021 (15:05:32)
% #k [setanimalstatus.m]: #n set a processing status tag for selected animal(s)
% The status tag appears in the left listbox (animals) and tooltip when hovering over the animal.
% #gw --> access via animal-listbox ⇒ context-menu/set status
%
% #ba 15 Sep 2021 (17:30:22)
% #k [anthistory.m]: #n load a project from history, i.a. from a list of previous ANTx calls/studies
% #gw --> access via ANT main GUI: ⇒ [green book]-button. Hit button to open the history.
%
% #ba 21 Sep 2021 (01:01:34)
% #k [DTIprep.m]: #n prepare data for DTI-processing via Mrtrix. Ideally DTI-processing could start
% after conventional registration of the "t2.nii" image to the normal space und running
% this DTIprep-step (a suitable DTI-atlas must be provided).
% shellscripts must be downloaded from https://github.com/ChariteExpMri/rodentDtiConnectomics
% and saved in the "shellscripts" folder (same level as the dat-folder)
% __current status__
% #n ☑ DTIprep for "single-shell" (single b-value diffusion acquisitions) analysis: finished + tested
% #n ♨ DTIprep for "multi-shell" analysis: has to be adjusted & tested!
% #gw --> access via ANT-menu: ⇒ Statistic/DTIprep for mrtrix.
% #ba 21 Sep 2021 (22:50:00)
% #k [DTIprep.m]: updated
% #n ☑ DTIprep for "multi-shell" (multi b-value diffusion acquisitions) analysis: finished
% -wrote some info/help to work with DTIprep.
% -added context menu (check b-table/DWI-files; delete files etc.)
%
% #ba 28 Sep 2021 (13:33:22)
% small changes in
% #k [uhelp] #n added: hyperlink selection via context menu
% #k [cfg_getfile2] #n added: 4D-Nifti filter
%
% #ba 29 Sep 2021 (17:11:33)
% Created a web-side with tutorials
% Depending on the time, further tutorials will be uploaded soon
% #gw --> access via link : <u>"https://chariteexpmri.github.io/antxdoc"
%
%
% #ba 01 Nov 2021 (17:29:22)
% #k [DTIprep] #n minor changes ..added some solutions to avoid some MRtrix-BUGs:
% --> see help of DTIprep.m
%
% #ba 27 Nov 2021 (23:15:21)
% #k [xgetparameter.m ] #n obtain mask-based parameter from images (multimasks & masks can be mulinary)
% mask-based paramters are: 'frequency' 'vol' 'mean' 'std' 'median' 'integrDens' 'min' 'max'
% MASK: you can use several masks/images, each with several sub-masks/(IDs), IDS across masks
% can be similar
% The output is one EXCELFILE containing sheets for each paramter. Each column contains the data of
% one of the selected animals. The output (excelfile) can be analyzed using MENU/STATISTIC/"label based statistic"
% .. CURRENTLY ONY PROVIDED FOR IMAGES/MASKS IN STANDARD-SPACE
%
% #ba 28 Nov 2021 (00:33:52)
% #k [xstatlabels.m] #n added tail-option for hypothesis-testing
%
% #ba 28 Nov 2021 (23:58:44)
% #k [xcreateMaps.m] #n create MAPS across animals (heatmaps/IncidenceMaps/MeanImage Maps etc)
% xcreateMaps.m: (former version "xincidencemap.m")
% choose a math. operation across images: {percent|sum|mean|median|min|max|sd|mode|rms|*specific*}
% #gw --> access via ANT-menu: ⇒ SNIPS/create Maps (incidenceMaps/MeanImage etc)
%
% #k [xrealign_elastix.m] #n --> replace NANs by Zeros in 4D-volume after realignment
%
% #ba 06 Dec 2021 (17:03:18)
% #k [cfm.m] #n --> case-file-matrix: visualize data (files x dirs), basic file-manipulation
% #gw --> access via ANT-GUI: Two new icons next to study-history-icon: CFM of all animals from
% the current study or CFM for selected animals (selected via left listbox)
%
% #ba 08 Dec 2021 (01:22:39)
% #k [xvol3d.m] #n save image as (tif/jpg/png) via context-menu (disable rotation-mode before access the context menu)
%
% #ba 20 Dec 2021 (14:42:46)
% #k [xstatlabels.m] #n The group-column in the "group-assignment"-Excel-file can be numeric now
%
% #ba 03 Jan 2022 (14:08:14)
% #k [xgetlabels4.m] #n A specifc fileName for resulting excel-file can be entered.
%
%
% #ba 06 Jan 2022 (13:37:22)
% #k [xcreateMaps.m] #n solved bugs:
% - selection of animals via left ANT-listbox before running this function enabled
% - previous image-operation "abs" ...sumation over images debugged. Note that this option produces the same
% result as the "sum"-operation.
% #gw --> access via ANT-menu: ⇒ SNIPS/Create MAPS
%
%
% #ba 12 Jan 2022 (17:12:52)
% #k [xstatlabels.m]: #n 'export' as excel-file now also contains the single animal data
% #k [xgetparameter.m]: #n added parameter "integrated density"
%
% #ba 14 Jan 2022 (12:03:50)
% #k [xdeformpop]: #n GUI was replaced by extended version (part of 'deform Volume Elastix'-operation)
% #k [xstat]: #n function was updated
% - The Powerpoint-report of the voxelwise statistic was extended
% - programmatically change viewing parameters / generate Powerpoint-report
%
% #ba 27 Jan 2022 (11:43:10)
% #k [xstat]: #n voxelwise analysis was extended.
% - post-hoc paramter modifications and summary report can executed from comandline
% - write summary as powerpoint-files, write statistical table as excel-file,
% - save statistically thresholded volume (Nifti)
% - button [code posthoc] display the code snippet for creating a summary (PPT-,Excel-,NIfti-files)
% #k [xstatlabels]: #n regionwise statistic was extended
% - The excelsheet now also contains a sheet "singleData" with the group-specifc single data for each region.
% The single data be further used for plots/visualization or other purposes
%
% #ba 06 Feb 2022 (21:18:33)
% function #k [getNiftiheader]: #n obtain NIFTI-header information of one/several NIFTI-files
% function #k [reslice_nii2]: #n reslice image by applying the header's transformation matrix
%
% #T 06 Feb 2022 (21:20:48)
% Updated the tutorial webside on Github-Pages. The Webside contains basic tutorials (PDF-files).
% #gw --> access via link : <u>"https://chariteexpmri.github.io/antxdoc"
% #gw --> access via ANT-menu: ⇒ EXTRAS/visit ANTx Tutorials (Github-Pages)
%
% #ba 08 Feb 2022 (12:38:25)
% function #k [exportfiles]: #n added as alternative to export/copy files from any data-hierarchie to
% a destination folder (no ANT-project must be loaded for this function)
% -function should also work for files of a studie's "dat"-folder
% #gw --> access via ANT-menu: ⇒ Main/export files (from any folder)
%
% #ba 11 Feb 2022 (00:31:35)
% small changes in #k [xdraw]: #n
% -debugged contour-fill and delete object (right-mouse click) functions
% #k [ant]: #n added resize buttons to animal listbox of the ANT gui. Resize the listbox in case of
% large cohorts or long animal names/identifiers
%
% #ba 23 Feb 2022 (16:40:25)
% function #k [DTIprep]: #n added a script-selection-option
% - scripts can be copied and costumized for own purpose
% - currently, there exist only three scripts:
% 1) "DTIscript_HPC_exportData_makeBatch.m"
% - script allows to export DTI-data to HPC-cluster storage, write a HPC-slurm batch & make batch executable
% - using "sbatch myBatchName.sh" the DTI-processing can be performed on the HPC-cluster
% 2) "DTIscript_posthoc_makeHTML_QA.m"
% - make HTML-file for quality assesment of DTI-processing (using png-images created by MRtrix)
% - this script ist for posthoc QA
% 3) "DTIscript_posthoc_exportData4Statistic.m"
% -post hoc file to export necessary files from HPC-cluster to another directory
% - script can be used for post-hoc statistical analysis
%
% #ba 02 Mar 2022 (16:17:11)
% function #k [xgetparameter]: #n extended
% - parameter-extraction now possible with animal-specific mask(s) located in the animal-folders
% potential scenario: parameter-extraction using animal-specific masks from read-out images
% in native space
% #ba 02 Mar 2022 (17:06:11)
% new tutorial #bw ["tutorial_extractParamter_via_Mask.docx"]
% This tutorial shows how to extract parameters (mean/volume etc.) from a read-out image
% using a mask. In this tutorial the mask contains two ROIs.
% #gw --> access via ANT-menu: Extras/documentations or ..\antx2\mritools\ant\docs
% #gw --> access via ANT-menu: ⇒ EXTRAS/visit ANTx Tutorials (Github-Pages)
%
%
% #ba 07 Mar 2022 (09:52:06)
% new function #k [scripts_gui]: #n This function contains a collection of scripts that can be
% costumized and applied. Currently the script-collection is available for the following functions:
% DTIprep.m; dtistat.m, xvol3d.m
%
% #ba 09 Mar 2022 (11:02:40)
% fixed bug in #k [exportfiles]: #n : subdir was not addressed correctly
%
% #ba 11 Mar 2022 (08:24:50)
% added a scripts collection to #k [xstat.m]: #n added scripts for voselwise statistic
% -scripts can be modified and applied
% -current scripts for voxwelwise statistic:
% 'VWscript_twosampleStat_simple.m'
% 'VWscript_MakeSummary_simple.m'
% 'VWscript_twosampleStat_severalimages.m'
% 'VWscript_MakeSummary_severalimages.m'
% 'VWscript_twosampleStat_severalimages_severalgroups.m'
% 'VWscript_MakeSummary_severalimages_severalgroups.m'
% #gw --> access via ANT-menu: ⇒ Statistic/SPM-statistic (or xstat.m) ⇒ use the [scripts]-button
%
% #ba 16 Mar 2022 (11:30:01)
% script "STscript_DTIstatistic_simple2.m" added to #k [dtistat.m]: #n
% This script performs the t-statistic (two groups) of the fibre-connections (*.csv-file)
% #gw --> access via ANT-menu: ⇒ Statistic/DTI-statistic (or dtistat.m) ⇒ use the [scripts]-button
%
% #ba 18 Mar 2022 (13:06:56)
% added to context menu of ANTx-animal listbox: checkRegistraton via HTML-file
% this option creates an HTML-file with the registration results for selected animals
% you can chose between
% -check forward registration (standard-space)
% -check specific forward registration (open GUI) --> you can specify specific paramters
% -check inverse registration (native-space)
% -check specific inverse registration (open GUI) --> you can specify specific paramters
% #gw --> ANTx-animal listbox ⇒ context menu
%
% #ba 23 Mar 2022 (00:37:51)
% different sorting strategies of the animals in the ANT-main GUI animal-listbox implemented
% 'default' : default sorting
% 'progress_down' or 'progress_up' : sort animals after atlas-registration-progress
% 'lengthName_up' or 'lengthName_down': sort animals after animal name length
% 'statusMsg_up' or 'statusMsg_down' : sort animals after status message (specified via context menu: "set status")
% #gw --> access via ANTx Gui pulldown-menu next to the [update]-button
%
%
% #ba 24 Mar 2022 (11:34:05)
% added "approach_photothrombosis" as option for elxMaskApproach
% This approach can be used for photothrombotic stroke models together with a lesionmask (with name 'lesionmask.nii')
%
% added #k [cleanmask.m]: #n This function can be used to delete slices from a NIFTI-image
% - currently this function can be used to delete errornuous slices from the "_msk.nii" image,
% generated from the skullstripping step. In some cases the registration (subsequent step) which
% depends on the "_msk.nii" is suboptimal. Thus use cleanmask.m to delete the affected slices from
% "_msk.nii"
% this function is still in progress...
% #gw --> ANTx-animal listbox ⇒ context menu /SPECIFIC TOOLS/prune mask ("_msk.nii")
%
% #ba 24 Mar 2022 (23:16:21)
% #k [cleanmask.m]: #n now also allows to remove tissue parts, help added
%
% #ba 04 Apr 2022 (13:54:22)
% added #k [HTMLprocsteps.m]: #n This function creates additional HTML-files for the
% processing report (initialization, coregistration, segementation and warping).
% These HTML-files are available as hyperlinks in the "summary.html"-report and depicts
% the output if each processing step for all animals. Thus you may not need to select the
% 'inspect'-hyperlink for each animal. Just select respective hyperlink to obtain an
% overview for all animals.
%
% #ba 05 Apr 2022 (12:39:20)
% added #k [scripts_collection.m]: #n This GUI contains scripts which can can be costumized
% The scripts-collection will be extended in the near future
% #gw --> access via ANT-menu: ⇒ SNIPS/scripts collection
%
% #ba 06 Apr 2022 (12:21:31)
% bugfix in #k [exportfiles.m]: #n ...internal file-filter was buggy
% bugfix in #k [xstat.m]: #n ... multifactorial design was buggy
%
% #ba 06 Apr 2022 (14:47:57)
% #k [antcb.m]: #n extended.. antcb('studydir') obtain study-folder
% [sdir sinfo]=antcb('studydir','info'); % obtain info for the study (storage-size/number of files/animals)
% see antcb('studydir?') for help
%
% bugfix in #k [sub_atlaslabel2xls.m]: #n ... removing default-sheets was not working
%
% #ba 06 Apr 2022 (17:39:47)
% #k [scripts_collection.m]: #n extended.. now contains the following scripts/examples:
% 'sc_xrename.m' .. shows how to rename files + basic file manipulation
% 'sc_register_to_standardspace.m' .. shows how to register 't2.nii' to standard-space
% 'sc_transformimage_exportfile.m' .. shows how to transform another image to standard-space & export files
% 'sc_checkregistrationHTML.m' .. shows how to generate HTMLfiles to check the registration
% 'sc_getantomicalLabels.m' .. shows how to extract anatomical-based parameters from images and save as excel-files
% #gw --> access via ANT-menu: ⇒ SNIPS/scripts collection
%
% #ba 11 Apr 2022 (12:23:25)
% #k [xstatlabels.m]: #n GUI was refreshed, added scripts-collection for xstatlabels
% -This function performes regionwise statistics of an image-parameter such as intensity mean or volume
% between groups
% #gw --> access via ANT-menu: ⇒ STATISTIC/label-based statistik
%
% #ba 27 Apr 2022 (17:30:24)
% #k [xbruker2nifti.m]: #n now supports comandline mode (silent/no GUI) with filter option
% -fun "selector2.m" supports preselection of rows
% -fun "lastmodified.m" added; return name and date of the last modified files of a directory and subfolders (sorted)
%
% #ba 28 Apr 2022 (13:43:07)
% #k [DTIprep.m]: #n prepare data for DTI-processing via Mrtrix. Ideally DTI-processing could start
% - added check and reordering optin for b-table & DWI-files
% #gw --> access via ANT-menu: ⇒ Statistic/DTIprep for mrtrix.
%
% #ba 29 Apr 2022 (08:23:36)
% #k [xbruker2nifti.m]: #n command line support was exteded (file filter options)
%
% #ba 04 May 2022 (14:53:04)
% antcb('selectdirs') command extended using filesearch-operation
% example: antcb('selectdirs','file',{'t2.nii' 'x_t2.nii'},'or'); %select all dirs containing either 't2.nii' or 'x_t2.nii'
%
% #ba 06 May 2022 (14:17:26)
% #k [updateantx.m]: #n noGUI-update/install function for antx-project via GITHUB (no graphical userinterface)
% -type "updateantx(2)" to just update local antx-toolbox
% -see help of updateantx.m for more information
%
% #ba 09 May 2022 (15:52:33)
% #k [xmaskgenerator.m]: #n implemented reslicing if another atlas is used with a different voxel-size
%
% #ba 11 May 2022 (00:08:32)
% #k [dispfiles.m]: #n display files folderwise in command-window (no GUI)
% examples with ant: dispfiles('form',2,'flt','.*.nii','counts',0);
% example no graphics support: dispfiles('form',2,'flt','.*.nii','counts',0,'dir',fullfile(pwd,'dat'));
%
% #ba 13 May 2022 (01:12:05)
% #k [xregister2d.m]: #n modified
% -runs on machines without graphic support
% -option to allow parallel processing over animals
% #k [xcoreg.m]: #n modified
% -runs on machines without graphic support
% -option to allow parallel processing over animals
%
% #ba 13 May 2022 (16:46:56)
% new tutorial #bw ["tutorial_noGraphic_support.docx"]
% This tutorial shows how to work on machines without graphic support and without GUIs
% 1) Optional: how to set the paths of elastix in unix/linux-system:
% 2) Optional: open interactive session on hpc-cluster and start matlab
% 3) Basics
% -add antx-paths
% -go to study-folder
% -update ant-toolbox
% -create a project-file:
% -load a project-file "proj.m"
% -check whether the project-file is loaded
% 4) Import bruker-data
% 5) Visualize files and folders
% 6) Selection of animals
% 7) Rename files
% 8) Register t2.nii to template (standard space, ss)
% 9) Extract the first 3d-volume from the 4d-vlume 'dti_b100.nii'
% 10) Coregister 'dti_b100_1stimg.nii' to t2.nii
% 11) Transform another image to standard-space
% 12) Transform another image to native-space
% 13) Check registration in standard-space - create html-file
% 14) Check registration in native-space - create html-file
% 15) REGIONWISE PARAMETER-EXTRACTION
% This tutorial shows how work without GUis or on machines without graphic support
% #gw --> access via ANT-menu: Extras/documentations or ..\antx2\mritools\ant\docs
% #gw --> access via ANT-menu: ⇒ EXTRAS/visit ANTx Tutorials (Github-Pages) https://chariteexpmri.github.io/antxdoc/
%
% #ba 16 May 2022 (16:13:10)
% [update]-button added next to [ant version]-button in ANTx-main gui
% The update button allows to retrieve the latest updates from GitHub
% (no GUis/no imput requested from user)
%
% #ba 17 May 2022 (00:20:29)
% #k [xgetlabels4.m] #n modified
% - get regionwise parameter now runs on HPC without GUI/graphic support ...
% see help of xgetlabels4.m ...Example-4
% - "hemisphere": 'separate' added to obtain region-wise parameters for each hemisphere separately
% in one run --> this results in two Excel-files (..left & ...right)
% - ["tutorial_noGraphic_support.docx"] was extended
%
% #ba 17 May 2022 (12:29:46)
% [update]-button: a context-menu was added
% - context menu options: update-info, force update, show last local changes, help on update
%
% #ba 23 May 2022 (16:16:07)
% #k [xrename.m] #n modified
% - added a file-filter
% - wildcard-option from command-line ..first tests
% - bug removed in context menu
%
% #ba 24 May 2022 (10:17:17)
% -embedded symbols changed in readme.md and antver.md (...seems no further support of placeholder service "via.placeholder.com")
%
% #ba 24 May 2022 (13:15:17)
% #k [cfg_getfile2.m] #n bug in filter-funtion removed
% #k [cfm.m] #n case-file matrix ...
% - copy/copy&rename (context menu) of files with different filenames in one step
% - delete files (context menu) with different filenames in one step
%
% #ba 25 May 2022 (11:44:39)
% #k [sub_atlaslabel2xls.m] #n - bug removed when writing xls-file
%
% #ba 28 May 2022 (18:20:48)
% #k [DTIprep.m] #n - preparation for DTI-processing
% - now works completely via command line (no-GUIs) --> see help DTIprep
% - sorting+matching of btables and DWIfiles enabled (please confirm visually!)
% - registration with parallel processing supported ...to enable change flag in the DTIconfig.m file in the DTI-folder
% - click DTIprep "scripts"-button to obtain an examle of DTIprep via COMMAND LINE ( #wm --> "DTIscript_runDTIprep_COMANDLINE.m")
%
% #ba 30 May 2022 (14:44:32)
% #k [DTIprep.m] #n - bug removed from CMDline-coregistration step
% The commandline tutorial #bw ["tutorial_noGraphic_support.docx"] was extended:
% the following steps where included
% 16) DTI-preprocessing: Import DTI/DWI-files from Bruker rawdata
% 17) DTI-preprocessing: rename DWI-files
% 18) DTI-preprocessing: A special DTI-atlas is needed
% 19) DTI-preprocessing: Perform DTI-preprocessing
% #ba 31 May 2022 (21:32:35)
% #k [scripts_gui.m] #n was modified
% - [scripts summary]-button added
% - scripts currently available for: [xstat.m], [DTIprep.m], [dtistat.m]
% - there is also a general scripts-collection: #gw --> access via ANT-menu: Snips/scripts collection
% #ba 01 Jun 2022 (14:39:14)
% #k [DTIprep.m] #n -scripts prettified
%
% #ba 02 Jun 2022 (16:51:58)
% #k [ant.m] #n was modified
% The menu of the ant-GUI is now sensitive to the pressed mouse-button:
% - [left mouseclick ] to execute the function
% - [right mouseclick] to display the underlying function in the CMD-Window with hyperlink to obtain the function's help
% - [cmd]+[left mouseclick ] to obtain the help of the function
%
% #ba 04 Jun 2022 (00:38:38)
% #k [ant.m] #n was modified
% - ANT-menu with optional tooltips for menu-items. Enable/disable tooltips via ANT-menu: INFO/"show menu items"
% -local ant-setttings enabled, this file can be stored in Matlab's userpath and will override default parameter
%
% #ba 09 Jun 2022 (16:36:28)
% #k [xnewgroupassignment.m] #n new function
% -create new group assignments by merging/combining different groups
% -the resulting excel-files (new group-assignment files) can be used as group-definition for:
% [DTIstat.m] --> statistic of DTI-connectome/metric
% [xstat.m] --> voxelwise statistic of images
% [xstatlabels.m] --> regionwise statistic of images
%
% #ba 10 Jun 2022 (16:44:06)
% #k [scripts_gui.m] #n modified
% -switch between scripts-collections via context-menu of upper listbox
%
% #ba 13 Jun 2022 (20:39:32)
% New tutorial #bw ["getOrientation_via_3pointSelection.pptx"]
% This tutorial shows how to determine the orientationType (for instance if method "examine orientation" failes)
% #gw --> access via ANT-menu: Extras/documentations or ..\antx2\mritools\ant\docs
% #gw --> access via ANT-menu: ⇒ EXTRAS/visit ANTx Tutorials (Github-Pages) https://chariteexpmri.github.io/antxdoc/
%
% #ba 14 Jun 2022 (14:20:14)
% #k [DTIprep.m] #n modified
% -'c_t2.nii' is not necessary for DTI-MRtrix-pipeline anymore
%
% #ba 15 Jun 2022 (00:42:12)
% New tutorial #bw ["tutorial_prepareDTIpipeline.docx"]
% This tutorial shows how to prepare the data for the DTI-MRtrix-pipeline
% #gw --> access via ANT-menu: Extras/documentations or ..\antx2\mritools\ant\docs
% #gw --> access via ANT-menu: ⇒ EXTRAS/visit ANTx Tutorials (Github-Pages) https://chariteexpmri.github.io/antxdoc/
%
% #ba 26 Jul 2022 (14:01:43)
% #k [xrename.m] #n modified
% -delete multiple files via wildcards via xrename
% #k [explorerpreselect.m] #n modified
% -explorerpreselect('mean.m') --> open folder in file-explorer containing and highlighting the m-file ('mean.m')
%
% #ba 02 Sep 2022 (08:55:09)
% #k [xexcel2atlas.m] #n modified
% -saveMasksSeparately: save output masks as separate NIFTIs
% #ba 27 Sep 2022 (13:51:29)
% #k [anthistory.m] #n modified
% a project can be found via "find"-button
% #ba 28 Sep 2022 (13:15:27)
% #k [xQAregistration.m] #n new
% calculate registration-based quality metric (standard-space comparison)
% -this procedure evaluates the animal registration quality to standard space
% -the [gm]-approach: the gray-matter compartement is warped to standard-space and compared with
% the gray matter image of the template (metrics: correlation or mutual information)
% -the resulting report is saved as HTML-file or excel-file
% #gw --> access via ANT-menu: GRAPHICS/QA:obtain registration metric
%
% #ba 11 Oct 2022 (14:01:29)
% [xrename.m] #n modified
% xrename now allows to modify the header of a NIFTI-file via 'ch:'-tag in the 3rd column
% header-modifications: use header of another file, change data type, dimensional flips, add header descrition
% see help of xrename
%
%
% #ba 21 Oct 2022 (14:21:05)
% task: generate DTI-atlas. A specific DTI-atlas can be gernated (with fewer regions)
% for this a modifed ANO-excelfile is saved and can be manually edited to include (include+merge) regions
% which should occur in the new DTI-atlas. In a second step this modifed ANO-excelfile can be used to generate
% a new DTI-atlas
% #gw --> access via ANT-MENU: atlas/masks / generate DTI-atlas / [1] save Atlas-file (excel-file) to manually include regions
% #gw --> access via ANT-MENU: atlas/masks / generate DTI-atlas / [2] generate DTI-atlas using the modified excel-file
%
% #ba 21 Oct 2022 (17:03:10)
% #k [xmakeRGBatlas.m] #n new
% function to convert an NIFTI-ATLAS to 4D-RGB-NIFTI file. This RGB-Atlas can be displayed for instance
% via "MRIcroGL" (https://www.nitrc.org/projects/mricrogl). Specifically for the Allen Brain atlas,
% the RGB-Atlas will depict the brain regions in the orignal Allen Colors similar to http://atlas.brain-map.org/atlas#atlas=1
% #ba 21 Oct 2022 (17:24:01)
% #k [xwarp3.m] #n modified
% image "t2.nii" stucked during coregistration to template-space due to potential NAN-values
% NAN-values are now replaces by "0"-values in the initialization-step
%
% #ba 25 Oct 2022 (17:09:33)
% #k [xvol3d.m] #n modified
% If a plot is generated via [xvol3d.m] the corresponding parameter settings can pasted to clipboard
% #gw --> access via xvol3d-MENU: props/"copy properties to clipboard"
% The property-list can be pasted into the editor, modified, saved and re-executed via xvol3d('loadprop',p); where p is the parameter-set
%
%
% #ba 30 Oct 2022 (23:17:02)
% #k [xexcel2atlas.m] #n modified
% removes any other characters in the new-ID column, hemispheric type 4 (both hemisphere, splitted) is used when not specified
%
% #ba 07 Nov 2022 (15:07:39)
% #k [xstat.m] #n removed bug when writing the NIFTI-file (issue with special characters)
%
%
% #ba 08 Nov 2022 (11:46:42)
% #k [antcb.m] #n added option to select/obtain list of animals by status-message
% example:
% - select all animals with status-tag "charge2":
% antcb('selectdirs','status','charge2');
% - select all animals with status-tag "charge1" or "charge2":
% antcb('selectdirs','status',{'charge1' 'charge2'});
% --> for further help type: antcb('selectdirs?')
%
% #ba 11 Nov 2022 (08:24:03)
% #k [ximportdir2dir.m] #n function revised
% - revised selection of directory-assignments
%
% #ba 11 Nov 2022 (17:10:28)
% #k [xstat.m] #n changed
% added function to posthoc create/repair the MIP-file/change Atlas for reporting table
% - see xstat-MENU: misc/create MIP,change Atlas
% - or programmatically, type : xstat('repairMIP?') to obtain help
%
% #ba 15 Jun 2022 (00:42:12)
% New tutorial #bw ["tutorial_voxwiseStatistic_independentTest.docx"]
% This tutorial shows how to perform Voxelwise statistic for two independent groups
% #gw --> access via ANT-menu: Extras/documentations or ..\antx2\mritools\ant\docs
% #gw --> access via ANT-menu: ⇒ EXTRAS/visit ANTx Tutorials (Github-Pages) https://chariteexpmri.github.io/antxdoc/
%
% #ba 30 Nov 2022 (00:00:04)
% #k [xexcel2atlas.m] #n modified
% - a HTML-file is additionally created to verify the regions of the new atlas
%
% #ba 01 Dec 2022 (13:53:56)
% #k [CTgetbrain_approach2.m] #n modified
% CT-segmentaton failed in some cases, ...hopefully solved now
% function is part of [xregisterCT.m] to rgister a CT-image to t2.nii
%
% #ba 09 Dec 2022 (09:21:47)
% #k [createGroupassignmentFile.m] #n modified
% The function create a group-assignment file (usefull for voxelwise statistic).
% with statistical models: 'unpaired', 'paired', 'regression', '1xANOVA', '1xANOVAwithin''fullfactorialANOVA'
%
% #k [xstat.m] #n modified and all models (with covaraiates) were simulated and checked
% tutorial needs to be updated and extended for the other statistical models
%
% #ba 13 Dec 2022 (13:04:03)
% minor bugs removed in #k [xstat.m] #n
%
% #ba 16 Dec 2022 (02:33:06)
% #k [CTgetbrain_approach2.m] #n modified
% CT-registration was checked using 6 datasets
%
% #ba 16 Dec 2022 (13:41:00)
% #k [xgroupassigfactorial.m] #n new
% assign new group-comparisons, create essential group-comparisons or manually via GUI
% input: excelfile with animal-ids and columns specifying the group-assignment for
% 1/2/3-factorial design. The output are excel-files with new group-comparisons
% #gw --> access via ANT-menu: ⇒ STATISTIC/NEW GROUP ASSIGNMENT
%
% #ba 16 Dec 2022 (14:09:43)
% #k [VWscript_DWIimages_and_results.m] #n new script
% script to make summary of voxelwise statistic FOR SEVERAL IMAGES
% #gw --> access via ANT-menu: ⇒ STATISTIC/SPM-STATISTIC .. via "scripts"-button
% #gw --> or type "xstat" --> "scripts"-button
%
% #ba 03 Jan 2023 (23:21:17)
% #k [xgroupassigfactorial.m] #n modified
% make specific group-comparisons via textfile
% modifed files:
% #k [paramgui.m] #n --> selection of multiple folders possible (via 'md')
% #k [xstat.m] #n --> append constrasts to multifactorial design via text-file ..see help of xaddContrasts.m
% #k [xaddContrasts.m] #n new file to append new contrasts to SPM-multifactorial design
% #ba 05 Jan 2023 (11:22:46)
% #k [xstat.m] #n modified: added option to delete existng contrasts
% #ba 06 Jan 2023 (08:38:39)
% #k [xdicom2nifti.m] #n modified: added option to use the DICOM-folderName as NIFTI-fileName
% % #ba 06 Jan 2023 (16:46:35)
% #k [xcheckreghtml.m] #n modified:
% -allows to specify colormaps for foreground and background-image
% -optional: a fused image of foreground and background-image is embedded in the HTMLfile
% #gw --> access via ANT-animal-listbox: ⇒ context-menu: "check registration-make HTMLfile"
% #gw --> access via ANT-menu: ⇒ GRAPHICS/"QA: generate HTML-file with overlays"
%
% #ba 10 Jan 2023 (01:48:56)
% minor checks
%
% #ba 16 Jan 2023 (15:30:39)
% #k [paramgui.m] #n modified:
% -added option to select a colormap from list of colormaps (colormaps appear color-coded in the pulldownmenu)
% -this option was implemented in xcheckreghtml.m
%
% #ba 16 Jan 2023 (23:56:39)
% #k [xrename.m] #n modified:
% -added: Replace value in 3d/4D image by another value
% -added: set voxe-size in image-header without changing the image
% -added: option to add a prefix or suffix to the orignal filename for the output image
% for examples see context menu/"enter 2nd and 3rd column extended"
%
% #ba 19 Jan 2023 (16:38:46)
% #k [dti_changeMatrix.m] #n modified:
% -DTI-weightmatrix can by changed via Excelfile containing the connections to keep
% -also possible via command-line (see help of [dti_changeMatrix.m])
% #gw --> access via ANT-menu: ⇒ STATISTIC/"DTI-statistic" --> via [change matrix]-button
%
% #ba 20 Jan 2023 (10:18:21)
% #k script: [DTIscript_exportToHPC_makeBatch.m] #n revised:
%
% #ba 07 Feb 2023 (22:25:52)
% #k [DTIprep.m] #n modified:
% B-tables are now accompanied by b-tables with fixed b-values ("grad*_fix.txt").
% The b-tables with fixed b-values will be used for MRtrix preprocessing only (dwifslpreproc/FSL-Eddy).
% Reason: Sometimes the large variation of b-values within the same shell leads to the FSL-Eddy error
% "inconsistent b-values detected". To circumvent this issue, the preprocessing uses the b-tables with
% fixed b-values. For further analysis steps the fixed b-values will be replaced by the original b-values.
%
% % #ba 13 Feb 2023 (12:30:06)
% #k [DTIprep.m] #n modified ...scripts added to see status of processing /delete MRtrix-related files
%
% #ba 14 Feb 2023 (17:37:59)
% #k script: [DTIscript_exportToHPC_makeBatch.m] #n revised again...
%
% #ba 20 Feb 2023 (23:22:40)
% #k new script: [DTIscript_DTIstatisticComplete1.m] #n
% -run DTI-statistic,create matrix-plots and ball-n-stick-plots, save plots as PPT, save tables as Excelfiles
% #gw --> access via MENU: Statistic/DTI-statistic (scripts-button) or type "dtistat" and hit scripts-button
% #ba 22 May 2023 (09:49:20)
% #k [xbruker2nifti.m] #n modified: option to add 'StudId' and 'SubjectName' as suffix to animal-directory name
% #ba 01 Jun 2023 (11:38:22)
% #k [xbruker2nifti.m] #n modified:
% -logfile for Bruker converted files is created for each animal
% -added example for Bruker conversion without GUI
% #k [xdraw.m] #n modified
% lesions can be delineated: First, preselect the animal folders, than go to #gw --> ANT-menu: ⇒ masks/"draw mask"
%
% #ba 12 Jun 2023 (18:53:05)
% #k [xgunzip2nifti.m] #n new, convert gzip-files to NIFTI-files within animal folders
% #gw --> access via ANT-menu: ⇒ Main/"convert gzip-files to NIFTI"
% #k [xobj2nifti.m] #n new, convert obj-files (Analyze) to NIFTI-files within animal folders
% #gw --> access via ANT-menu: ⇒ Main/"convert obj-files to NIFTI"
% reference image can be used to replace header
% #k [xmergemasks.m] #n new, merge multiple masks within animal folders
% #gw --> access via ANT-menu: ⇒ atlas+masks/"merge masks"
% #ba 13 Jun 2023 (12:04:18)
% #k [paramgui.m] #n, added 2D-cell pulldown
% % #ba 16 Jun 2023 (16:11:44)
% #k [xdraw.m] #n refurbished
% contour-line filling: borders can be added to contraint the filling
% added simple drawing tool
% #ba 12 Jul 2023 (08:53:34)
% #k [xmakepseudoatlas.m] #n new, create pseudo-color NIFTI-atlas based on existing NIFTI-ATLAS
% rationale: atlases such as the Allen brain atlas use sparse IDs over a large dynamic range.
% This is sometimes not optimal for displaying atlas
% #gw --> access via ANT-menu: ⇒ atlas+masks/"create pseudo-color atlas"
%
% #ba 13 Jul 2023 (08:51:56)
% [P28 developing mouse template] added to gdrive
% this is a modified version of the Allen developing mouse atlas
% - Paper : David M Young, Siavash Fazel Darbandi, Grace Schwartz, Zachary Bonzell, Deniz Yuruk, Mai Nojima, Laurent C Gole, John LR Rubenstein, Weimiao Yu, Stephan J Sanders (2021) Constructing and optimizing 3D atlases from 2D data with application to the developing mouse brain eLife 10:e61408
% https://doi.org/10.7554/eLife.61408
% https://elifesciences.org/articles/61408
% - #gw --> access via link : https://drive.google.com/drive/u/2/folders/1q5XOOVLvUYLqYsQJLqNRF7OK8fNwYhI9
%
% #ba 30 Aug 2023 (15:37:19)
% script: VWscript_DWIimages__oneWayANOVA.m added to scripts-collection (avaliable from xstat.m)
% #ba 07 Sep 2023 (12:27:25)
% new script "DTIscript_exportToHPC_makeBatch_07-09-2023.m" added. Script exports dti-data to HPC for preprocessing
% script works with SLURM-JOB-ARRAY (parallelized) due to restricted proc-time (max 48h) on CHARITE-HPC
%
% #ba 15 Sep 2023 (13:10:51)
% #k [dtiPREP.m] #n modified, new option: transfer GM,WM,CSF-mask to MRtrix-pipeline
%
%
% #ba 21 Sep 2023 (22:43:56)
% antconfig/project-file modified,
% optional mode for initial skull stripping via otsu method (x.wa.usePriorskullstrip = [5])
%
% #k [xgetlabels4.m] #n modified,
% different output-formats (.xlsx, .mat, .csv) now available
%
% #ba 20 Oct 2023 (10:17:42)
% script [DTIscript_exportToHPC_makeBatch_07-09-2023.m] created
% reason: conda-path changed on our HPC
% #ba 09 Nov 2023 (12:42:50)
% #k [renameDWIfiles.m] #n new, function to check and rename DWI-files across animals
% case: different scan-numbers in DWI-filenames across animals
% -available via DTIprep-GUI, [check DWI-filename]-button
% #ba 13 Nov 2023 (01:09:12)
% #k [xcoreg2D_singleSlice.m] #n new function: coregister 3D-images using 2D-registration of a specified slice
% and apply transformation parameters to all other slices.
% #gw --> access via ANT-menu: ⇒ 2D/"single slice 2D-registration"
% #ba 23 Nov 2023 (14:08:03)
% #k [xgetpreorientAuto.m] #n new, get studies "t2.nii" pre-orientation automatically
% -available via ANTx animal-listbox context menu, [get orientation -automatic mode]
%
% #ba 05 Dec 2023 (23:25:04)
% #k [ximportBrukerNifti.m] #n new, import existing NIFTI-files from Brukerdata.
% -available via ANTx menu Main/Import existing NIFTI-files from Bruker data
%
% #ba 11 Dec 2023 (12:26:44)
% #k [ximportBrukerNifti.m] #n modified ...noGUI-mode enabled (see last example on HELP of DTIprep.m )
%
% #ba 12 Dec 2023 (14:09:47)
% #k [xrename.m] #n added option to run operation(mean/median/mode/sum/min/max/std/zscore/var) over 4th dim of NIFTI-file
%
% #ba 20 Dec 2023 (14:00:20)
% #k [xgetpreorientationHTML] #n new, obtain pre-orientation (the "pre-alignment task") via HTMLfile
% -The output ia a HTML-file in the study's 'checks'-folder. The HTML-file contains different orientations of the source-image.
% To obtain the pre-orientation from native-space to standard-space:
% #gw --> access via ANTx animal-listbox context menu: ⇒ [examine orientation via HTMLfile]
% For any other images with different orientations:
% #gw --> access via ANT-menu: ⇒ Tools/"obtain pre-orientation (via HTMLfile)"
%
% #ba 12 Jan 2024 (12:55:22)
% #k [DTIprep.m] #n modified, check Number of b-values and number of DWI-volumes
%
%
% #ba 26 Jan 2024 (15:41:27)
% #k [xvol3d] #n modified, parameter-settings for displaying atlas-regions can be stored as script
% and the same plot can be re-created
% -a sccript "vol3dscript_loadMask_Atlas_Regions_SaveImages.m" can be used from the "scripts"-menu
% of xvol3d-GUI. To store a parameter-settings after finalizing the plot use "probs"-menu/copy-properties-to clipboard
%
% #ba 31 Jan 2024 (16:50:36)
% #k [xoperateMaps] #n new
% arithmetic operations (add,subtract,multiply,divide) two maps (heatmaps/incidenceMaps/etc)