Final test #1
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Final test #1
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cmadjar
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Feb 24, 2021
cmadjar
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Mar 15, 2021
* Adding -uploadID option to minc_insertion.pl * Read file types from the DB instead of the hardcoding it in the code * Updated the regex to include an optional .gz extension when determining the file type * Stopped when testing extraction of the archive. For some reason it fails, out of memory... * Modified imaging_upload_file.pl to include PET modality * Adding PET HRRT script * A few more lines of code * Reading HRRT study * Saving missing files (SQL and HRRTSUM library) * More lines of code. * Almost finished the pipeline. Need to test minc_insertion.pl command: minc_insertion.pl -profile prod -mincPath/data/incoming/preventAD/MTL0661_603347_PREPT00_NAV_small/MTL0661_603347_PREPT00-NAV-HRRT1030-2017.3.16.12.3.14_EMMASK_3D.mnc -acquisition_protocol F18NAV6frOSEM -bypass_extra_file_checks Then need to: - find a way to link the ecat data in parameter file - call mass_pic.pl - call mass_jiv.pl - implement an ImagingUpload function that calls HRRT_PET_insertion.pl with proper argument (included set BIC flag) - proper logging and exit codes - clean up the todo item modified: HRRT_PET_insertion.pl modified: NeuroDB/HRRTSUM.pm * Adding -uploadID option to minc_insertion.pl * Moved around functions in proper libraries Inserting MINC file from HRRT scanner into the database minc_insertion.pl working. Left to add a link from files to hrrt_archive. SQL modified, need to modify the scripts in consequence. Adding HrrtArchiveID into the files table and adding a link to the ecat file into the parameter_file table Making that all call to modified functions with upload_id instead of archive source location are modified to include $upload_id Instead of using getUploadIDUsingTarchiveSrcLoc for all functions of MRIProcessingUtility, passing the uploadID to those functions to simplify the code Update hrrt_archive and mri_upload tables at the end of HRRT_PET_insertion.pl execution Fixed a conflict badly resolved and uncommented big part of the script that were commented for testing A few more changes to the HRRT_PET_insertion.pl script incorporating the exit codes into the PET pipeline Fixing one of the exit code and adding description for the new script Removed columns from hrrt_archive and modified hash technic from MD5 to BLAKE2 Changed the way we identify the uploaded study is from an HRRT scanner Removed the modality from the Schema changes Fixing the exit codes for imaging_upload_file.pl and ImagingUpload.pm Solved exit code duplication, removed extra print and change mod of HRRT_PET_insertion.pl so can be called from imaging_upload_file.pl remove unrelated changes due to rebase remove unrelated changes due to rebase cleanup finished cleanup of rebase hopefully finished cleanup of rebase hopefully moved some functions to HRRT a few improvements modifed the profileTemplate.pl fixed a bug in mri_upload update fix bug in imaging upload fixed a few bugs * removed the SQL from that PR now that one was sent on the LORIS side * finished writing documentation in the perl scripts * updated the documentation * PetHRRT pipeline fixes * PetHRRT pipeline fixes (#1) * PetHRRT pipeline fixes (v3) * PetHRRT pipeline fixes (v4) * fixes failure to insert into parameter_file due to bad encoding of some values from the mincheader... Co-authored-by: Laetitia Fesselier <laetitia.fesselier@mail.mcgill.ca>
cmadjar
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Oct 6, 2021
* script and SQL patch to convert CBIGR scans to BIDS * remove the two .idea files from git * fix T2star BIDS naming * resolve the problem with run numbers being incorrect for acquisitions with phase and magnitude images * add support email Co-authored-by: Krishna Chatpar <krishna.chatpar@mcgill.ca>
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