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[post 19.0.0 release] loris-mri-docs: forward changes from v19.0.0 an…
…d resolve conflicts (#280) * Initial import of files from http://code.google.com/p/dicom-archive/ * add two configurable options is_site and is_sge * Added new getIncomingDir config function * Added missing semi-colons. * Modifies the temporairy values of $data_dir, $get_dicom_info and $mail_user variables * Places back the forward slash in the email-address * Modifies the temporairy value for the tarchive_librairy location * Modified the tarchivelibdir temp value * Set the if_sge to false by default * Fixed the dcmodify --insert-tag option to --insert (option used in more recent dcmodify). * Updates the mri_upload table * Includes option to update the mri_upload table * Modification to the profileTemplate to be able to use DTIPrep pipeline * Added get_DTI_Site_CandID_Visit function in profile file * Cosmetic changes * Cosmetic changes * Fixed typos and indentation * Correct spelling mistakes * 1) added the functionality to insert the extension , 2) fixed indentation * Removed the filetype option * Changed the queries to use the prepared statements * Modified $d to $dir in profileTemplate * Remove .DS_Store file from DICOM source directory before creating new object. Other fails while reading content of dcm source directory * Modified getSubjectIDs so that it uses PatientName instead of PatientID lookupCenterID using patient name instead of PatientID * modified: profileTemplate * Moved reference to ~/.neurodb to .loris_mri directory * Some more files * Replaced .neurodb by .loris_mri in updateHeaders.pl * Removed the full path * DicomTar.pl should use proper $profile name instead of prod * Sometime DICOM Header may not have Invertion Time field (0018,9079). Set Inversion Time to 0 in tarchive_series to avoid error message: DBD::mysql::st execute failed: Data truncated for column 'InversionTime' * DICOM HEADER may not have Inversion time (0018,9079) set which cause tarchives_series sql table who expect a double to receive an empty string. * THIS IS A DUPLICATE from opionnalProfileFixInDicomTar pull request please ignore change in dicomTar.pl THIS IS A DUPLICATE from opionnalProfileFixInDicomTar pull request please ignore change in dicomTar.pl * removed useless numbers * Added $subjectID{'createVisitLabel'} option to profile template. * Changed $subjectID{'createVisitLabel'} type to boolean * added exit 0 at the end of the file * cosmetic change * Added a new option config $bin_dir * Fixed the option * Defined(@array) is deprecated. Removed error message on the console defined(@array) is deprecated at... (Maybe you should just omit the defined()?) * Removed all occurences of defined(@array). * replaced the sourcelocation column by DecompressedLocation * Added functionality to insert PET DICOMs in tarchive tables. * Fixed indentation in the pull request. * NIfTI support of the imaging pipeline (profileTemplate change). * Added -centerName option in call to dicomTar.pl. * Made ArchiveLocation relative in tarchive table. * Created a MySQL scripted patch to make ArchiveLocation in the tarchive table relative. * Added functionality to print query on one line. * Cleaned up and prepared statement for queries in main directory of dicom-archive-tools * Prepared mysql statement for DCMSUM.pm * Fixed bug inserted while integrating mysql prepare statements * Removed the Deprecated definition of array: !@Settings instead of !defined @Settings, to be in line with pull request #95 * One more consistency check on verbose and notification spool tables * One more explicit Done message * Fixes the insert in DCMSUM.pm so it does not set the creatinguser field in the tarchive table to NULL when the pipeline is run in auto-launch mode. * site or rather, study, no longer hard coded * removed extra ~ and the comments as per Cecile feedback * adding TarchiveSeriesID to the tarchive_files * Added the getSNRModalities function * added flair * typo * typo AGAIN * added comment based on SeriesUID and EchoTime * Removed getIncomingDir routine from profileTemplate; it is no longer used. Same as PR35 * Revert "adding TarchiveSeriesID to the tarchive_files" * isFileToBeRegisteredGivenProtocol in Profile now returns 1 if ne unknown * Incorporate comment of Dave * I cna not type wihtout making typos * re-adding TarchiveSeriesID to the tarchive_files * swap inserts * added comment * updated the comment with tarchive_files * Loris-MRI configurations moved to the front end from the $profile file: Redmine 8893 (#182) * Loris-MRI configurations moved to the front end from the $profile file: Redmine 8893 * went through all the files that get the settings from the prod file * added the install scripts * removed prefix from the Get_DTI_Site function * added data_dir as projects like IBIS could have it different from mincPath * Greg feedback on DB::DBI, removal of defined, and a masked variable declaration * added the script for existing projects to populate their default database values with those from their prod file * function return value * IBIS has all sorts of differences, the updates in this commit account for those * data_dir renamed to dataDirBasepath * Cecile feedback and applying her comments to all other files * fixed the message where the values is kept at its default, and removed debug print * Loris-MRI configurations moved to the front end from the $profile file: Redmine 8893 (#45) * Loris-MRI configurations moved to the front end from the $profile file: Redmine 8893 * went through all the files that get the settings from the prod file * removed prefix from the Get_DTI_Site function * consistency in DB versus NeuroDB * one dollar sign instead of 2; but have no clue why * Cecile required changes * [ImagingUpload.pm] Look inside file type and not file path for the word dicom (#178) * Look inside file type and not file path for the word dicom * check for the whole dicom type string * spaces * spaces * Fix file count in mri_upload when deleting a minc file and then re-inserting (#180) * fixed minc deletion (#185) * Remove all .DS_Store files anywhere in the tree, and __MACOSX directory (#46) * Remove all .DS_Store files anywhere in the tree * The command will not complain even if it does not find a file to delete. * Incorporate the additional changes from Mouna * Removed files starting with . and __MACOSX directory from the uploaded scans: Redmine 11670 (#186) * started * first attempt finished * cleanup * included mounas feedback * Updating README with proper dpkg (#190) * [Installation] Fixing more installation errors (#191) * Fixing more errors * This will be much clearer * changed new_nmi to nmi * missed one :p * [SQL] Fixing MySQL 5.7 group by during visit creation (#192) * Fixing MySQL 5.7 group by during visit creation * Missed comma * Removing newVisitNo in group by * Added option to also re-insert deleted minc files (Same as PR#179) (#193) * added option to also re-insert * Remove profile changes * removing IBIS specific fields * No need to show another example of sql query * adding documentation and making sql more generic * more updates * fix path to run from mri directory * Option to re-insert deleted minc files: Based off of PR 179 * remove the original file * better readme * Cecile comments * relative to example scripts directory * Modified the deletemincsqlwrapper.pl so that when no files are found with the query, it prints it out so that the user do not feel like nothing happened. * revert to t1 from adniT1 * remove the wrong file * minor thing * chmod, run tarchiveLoader without seriesUID as an argument, and small messages change * [Install] Readme Version update, installer CentOS improvements (#188) * committing Readme version and installer changes * adding Readme changes * setting VERSION file to 18.0.0 * additional Readme updates * formatting in Readme * re-integrating updates * removing period * New installs now also have their Imaging Pipeline ConfigSettings populated based on the user answers during the installation process: Redmine 13199 * minor echo message change * rebasing removed Christine changes so add them again * update the dicom archive repo link (#199) Update submodule link for dicom_archive. * Do not store PatientName header in notification_spool table:Redmine 13506 * update README * Check consistent upload_id and filename when running the pipeline: Redmine 13507 (#202) * Check consistent upload_id and filename when running the pipeline: Redmine 13507 * make copy and paste a bit more intelligent * Mapping empty date of birth and scan to undef when empty so that it can be inserted in MySQL 5.7 (#205) * Creected code that tests if two float numbers are equal (#206) * [Cleanup]: Remove duplicate DBI.pm; Redmine 13613 (#207) * Add TarchiveID to mri_protocol_violated_scans (#211) * Adding TarchiveID information in mri_protocol_violated_scans table * Cleaned up commented parts * Renamed $tarchiveInfo to $tarchiveInfoRef for consistencies * Get file list after removal of undesired directories like __MACOSX: Redmine 13508 (#203) * Get file list after removal of undesired directories like __MACOSX: Redmine 13508 * change xargs to deleting from the find command * Dave and Nick feedback * Nicolas feedback; escaping the directory name * Refactor smart matching code in DTI.pm (#215) * Better MINC toolkit sourcing command in README and updated VERSION file (#260) * Better MINC toolkit sourcing command and updated VERSION file * cecile feedback * Updating QC tables if the -deleteQCdata flag is not set. Will update FileID to NULL in files_qcstatus and feedback_mri_comments (#261) * README has also within it LORIS-MRI version number, so update (#268) * Installer: Populate the default LORIS config settings for the MRI paths (Redmine 13915) (#272) * Populate Loris-MRI code path for new installs since the user is asked to enter the MRI project name * Populate other MRI data path with a better option than the default LORIS %PROJECTNAME * post installation checks * Add the condition Dave brought up during the imaging meeting; i.e. only change it for those that did not do it in the front end already * Ceciles feedback * oopsie * resolve some unresolved conflicts and remove all added empty lines * Ceciles feedback to remove duplicate getconfigsetting * feedback after discussing with Nick
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