Colorization and Automated Segmentation of Human T2 MR Brain Images for Characterization of Soft Tissues

Characterization of tissues like brain by using magnetic resonance (MR) images and colorization of the gray scale image has been reported in the literature, along with the advantages and drawbacks. Here, we present two independent methods; (i) a novel colorization method to underscore the variability in brain MR images, indicative of the underlying physical density of bio tissue, (ii) a segmentation method (both hard and soft segmentation) to characterize gray brain MR images. The segmented images are then transformed into color using the above-mentioned colorization method, yielding promising results for manual tracing. Our color transformation incorporates the voxel classification by matching the luminance of voxels of the source MR image and provided color image by measuring the distance between them. The segmentation method is based on single-phase clustering for 2D and 3D image segmentation with a new auto centroid selection method, which divides the image into three distinct regions (gray matter (GM), white matter (WM), and cerebrospinal fluid (CSF) using prior anatomical knowledge). Results have been successfully validated on human T2-weighted (T2) brain MR images. The proposed method can be potentially applied to gray-scale images from other imaging modalities, in bringing out additional diagnostic tissue information contained in the colorized image processing approach as described

aces/Loris: LORIS Release v24.1.3

This releases fixes bugs that were discovered since the v24.1.2 release. Most notably: [issue_tracker] Make Comments and History easier to read #8370 [document_repository] Fix download path to correct user #8378 [media] add feedback to dropdown field when is empty #8402 [imaging_browser] Fix control panel positioning #8424 [examiner] Remove link to edit examiner if certification is not enabled #8425 [SQL] Fix 23 Cleanup patches #8430 [Build] apt deps issue #8431 [dqt] Fix loading saved query #8436 [SQL] 24.0.0 release patch fix truncation error #8438 [Genomic Browser] UserSiteMatch fix #8468 [SQL] Fix hardcoded parent ID for IssueTrackerDataPath in patches #8475 </ul

aces/Loris: LORIS Release v24.1.6

&lt;h2&gt;What's Changed&lt;/h2&gt; &lt;ul&gt; &lt;li&gt;[issue_tracker] Do not display inactive users in issue form by @charlottesce in https://github.com/aces/Loris/pull/8841&lt;/li&gt; &lt;li&gt;[LINST] skip metadatafields for surveys by @zaliqarosli in https://github.com/aces/Loris/pull/8961&lt;/li&gt; &lt;li&gt;[tools] Fix efficiency of fix_candidate_age script by @CamilleBeau in https://github.com/aces/Loris/pull/8992&lt;/li&gt; &lt;li&gt;[media] fixes issue when media module try to instantiate a non existing instrument. by @racostas in https://github.com/aces/Loris/pull/8903&lt;/li&gt; &lt;li&gt;[LINST] fix survey and date issues by @ridz1208 in https://github.com/aces/Loris/pull/8858&lt;/li&gt; &lt;li&gt;[JSX] Modal Width Prop by @skarya22 in https://github.com/aces/Loris/pull/8893&lt;/li&gt; &lt;li&gt;[libraries] Get examiner sites by UserID by @CamilleBeau in https://github.com/aces/Loris/pull/8994&lt;/li&gt; &lt;li&gt;[genomic_browser] Download button not showing up in the Files tab by @ridz1208 in https://github.com/aces/Loris/pull/8480&lt;/li&gt; &lt;li&gt;[issue_tracker - raisinbread/tools] Fix issue tracker history wrong module ID by @zaliqarosli in https://github.com/aces/Loris/pull/8677&lt;/li&gt; &lt;li&gt;[Issue Tracker] Issue Change Notifications by @skarya22 in https://github.com/aces/Loris/pull/8885&lt;/li&gt; &lt;li&gt;[behavioural_qc] fixes visitLevel feedback not showing up. by @racostas in https://github.com/aces/Loris/pull/8900&lt;/li&gt; &lt;/ul&gt; &lt;p&gt;&lt;strong&gt;Full Changelog&lt;/strong&gt;: https://github.com/aces/Loris/compare/v24.1.5...v24.1.6&lt;/p&gt

aces/Loris: LORIS Release v24.1.2

This releases fixes bugs that were discovered since the v24.1.1 release. Most notably: [SQL] Reorder release patches for 24.0 release #8390 [Performance] Do not load module logger from constructor #8200 Download NIfTI file from imaging browser when a NIfTI file is available in addition to a MINC file #8206 [behavioural_qc] Fix critical error #8245 [issue tracker] Email watchers when issue is updated or created #8248 [core] return error message on invalid dob (rebase 24.1) #8279 [core] Fix incorrect message/error for instrument access #8284 [tools] Fix path in recreate_conflict #8292 [issue tracker] Fix emailing bug found in HBCD #8300 [issue_tracker] make assignee drop down not required #8301 [issue tracker] Fix issue description #8351 [imaging browser] Fix download of JSON, Bval and Bvec files when they are on s3 #8354 [imaging browser] Fix Human dangling out of nowhere #8363 [NDB_BVL_Instrument] Add get function to access protected selectMultipleElements #8381 [CSS/instruments] Fix control panel position when scrolling #8383 [MRI Violations] Fixes links to BrainBrowser from the MRI violations module #8392 Update CONTRIBUTING.md #8421 Full Changelog: https://github.com/aces/Loris/compare/v24.1.1...v24.1.2 Upgrade Process from version 23.X.Y to 24.1.2 (amendments) Note: The instructions below REPLACE the instructions in the release notes of released versions 24.0.0 AND 24.1.0. The instructions in those releases should be disregarded. 23.x.y to 24.0.0 Get the 24.1.2 source code Source the SQL/Release_patches/23.0_To_24.0_upgrade_A.sql SQL file into your database. Run the following scripts: php tools/configuration_check.php This script is used to validate the configuration of LORIS. It checks configuration settings and server paths to make sure that the application and underlying architecture are set up to allow LORIS to run properly. php tools/single_use/SaveUserIDToInstrumentData.php confirm This script is intended for a one-time use only to restore the value of the UserID column of instrument tables and the UserID key of the instrument JSON Data in the flag table. php tools/single_use/remove_publication_users_edit_perm_rel_duplicates.php _This script deletes duplicate rows in publication_users_edit_perm_rel to make sure the patch '2020-01-07-publication_users_edit_perm_relpk.sql' will execute successfully php tools/single_use/Cleanup_Special_Chars_Document_Repository.php This script is written to clean up the files with special characters from the document repository data table as well as clean up the quotes appearing as %22 in the file names in the file system php tools/single_use/Cleanup_Special_Chars_Media.php This script is written to clean up the files with special characters from the media data table as well as clean up the quotes appearing as %22 in the file names in the file system php tools/single_use/Remove_duplicate_examiners.php This script is written to clean up duplicate userIDs in the examiners table Make sure the RegistrationProjectID column in the candidate table of the dataabse does not contain any NULL values. If it does, either assign an existing project to the candidate/scanner or create a new project for these entries before running the release patch (see "Notes for existing projects" for more details). Source the SQL/Release_patches/23.0_To_24.0_upgrade_B.sql SQL file into your database. Run the following scripts: php tools/single_use/populate_visits.php _This script populates the visits table based on the config.xml, session table and Visit_Windows table._ php tools/single_use/Set_Required_elements_completed_flag.php confirm _This script is written to migrate the Data_entry_completion_status field from the instrument table (or Data column of the flag table) to it's own column in the flag table called Required_elements_completed. Note that this script can take a long time to complete on large projects._ Run make all on the LORIS root directory OPTIONAL: Source SQL patches from the SQL/Archive/24.0/Cleanup directory at your discretion to remove superfluous or deprecated entries in the database. OPTIONAL: Run the tools/single_use/Remove_Data_entry_completion_status_instr_column.php PHP script to generate an SQL patch containing all DROP COLUMN statements for the now unused Data_entry_completion_status field in instruments. This script will generate the SQL patch and store it in the SQL/Archive/autogenerated/single_use/ directory under the name Remove_Data_entry_completion_status.sql. OPTIONAL: Remove the &lt;visitLabel subprojectID="X"&gt; tags in the Config.xml file *NOTE: The tools/single_use/SaveUserIDToInstrumentData.php can take several hours up to a day to run depending on the size and age of the databse and number of instruments used* 24.0.0 to 24.1.2 Source the SQL/Release_patches/24.0_To_24.1_upgrade.sql SQL file into your database. If you have LORIS-MRI installed, make sure to upgrade LORIS-MRI to 24.1.0 since the SQL changes will affect the MRI insertion scripts. </ol

LORIS (Longitudinal Online Research and Imaging System)

&lt;h2&gt;What's Changed&lt;/h2&gt; &lt;ul&gt; &lt;li&gt;[media] React Warning on Upload Tab by @skarya22 in https://github.com/aces/Loris/pull/8721&lt;/li&gt; &lt;li&gt;[issue_tracker] Do not display inactive users in issue form by @charlottesce in https://github.com/aces/Loris/pull/8841&lt;/li&gt; &lt;li&gt;[LINST] skip metadatafields for surveys by @zaliqarosli in https://github.com/aces/Loris/pull/8961&lt;/li&gt; &lt;li&gt;[dictionary] Fixes for correct displaying &quot;Data Type&quot; column for the enumeration type in the &quot;Data Dictionary (Beta)&quot; table by @yagurdmitriy in https://github.com/aces/Loris/pull/8976&lt;/li&gt; &lt;li&gt;[tools] Fix efficiency of fix_candidate_age script by @CamilleBeau in https://github.com/aces/Loris/pull/8992&lt;/li&gt; &lt;li&gt;[media] fixes issue when media module try to instantiate a non existing instrument. by @racostas in https://github.com/aces/Loris/pull/8903&lt;/li&gt; &lt;li&gt;[instrument_list] Fix deprecation warning by @driusan in https://github.com/aces/Loris/pull/8867&lt;/li&gt; &lt;li&gt;[LINST] fix survey and date issues by @ridz1208 in https://github.com/aces/Loris/pull/8858&lt;/li&gt; &lt;li&gt;[JSX] Modal Width Prop by @skarya22 in https://github.com/aces/Loris/pull/8893&lt;/li&gt; &lt;li&gt;[libraries] Get examiner sites by UserID by @CamilleBeau in https://github.com/aces/Loris/pull/8994&lt;/li&gt; &lt;li&gt;[genomic_browser] Download button not showing up in the Files tab by @ridz1208 in https://github.com/aces/Loris/pull/8480&lt;/li&gt; &lt;li&gt;[issue_tracker - raisinbread/tools] Fix issue tracker history wrong module ID by @zaliqarosli in https://github.com/aces/Loris/pull/8677&lt;/li&gt; &lt;li&gt;[Issue Tracker] Issue Change Notifications by @skarya22 in https://github.com/aces/Loris/pull/8885&lt;/li&gt; &lt;li&gt;[behavioural_qc] fixes visitLevel feedback not showing up. by @racostas in https://github.com/aces/Loris/pull/8900&lt;/li&gt; &lt;li&gt;[battery_manager] Update Test Plan by @skarya22 in https://github.com/aces/Loris/pull/8782&lt;/li&gt; &lt;/ul&gt; &lt;h2&gt;New Contributors&lt;/h2&gt; &lt;ul&gt; &lt;li&gt;@yagurdmitriy made their first contribution in https://github.com/aces/Loris/pull/8976&lt;/li&gt; &lt;/ul&gt; &lt;p&gt;&lt;strong&gt;Full Changelog&lt;/strong&gt;: https://github.com/aces/Loris/compare/v25.0.1...v25.0.2&lt;/p&gt;If you use this software, please cite it using these metadata