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jvs:fscan:manual:chapter2:invivo [2013/08/12 16:03] voyvodic created |
jvs:fscan:manual:chapter2:invivo [2014/03/24 18:37] voyvodic |
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===== Table InVivo -- Special case InVivo data tables ===== | ===== Table InVivo -- Special case InVivo data tables ===== | ||
**usage:** | **usage:** | ||
- | * **-table invivo | + | |
- | * **-table invivo | + | * -table invivo |
- | * **-table invivo | + | * -table invivo |
- | * **-table invivo TBLNAME 4 NAME**\\ | + | |
- | * **-table invivo TBLNAME 5 NAME**\\ | + | |
- | * **-table invivo TBLNAME 6 NAME**\\ | + | |
- | * **-table invivo TBLNAME 7 NAME**\\ | + | |
- | * **-table invivo TBLNAME 8 NAME**\\ | + | |
- | The TABLE INVIVO command | + | The TABLE INVIVO command |
+ | STUDYTABLE is the name of the data table being manipulated. In general this table should already exist (i.e., created by a previous [[jvs: | ||
+ | |||
+ | ==== Mode 1 - find recently modified studies and update series tables ==== | ||
+ | Look through STUDIESDIR to find series with DICOM files. | ||
+ | Consider only studies with StudyDir or StudyDir/ | ||
+ | Find first DICOM file for each series to get patname, ID, date, time, etc fields | ||
+ | |||
+ | ==== Mode 2 - create local BXH header files for each series in qualifying studyies ==== | ||
+ | For each series, created DICOM file table, sort by imgnum, then create BXH file. | ||
+ | |||
+ | FLAG: | ||
+ | * 1-7 - downsampling by this many images (default=5) | ||
+ | * 8 - downsample 500+ series lists if NIMGS > 50 | ||
+ | * 16 - downsample any DICOM series if NIMGS > 50 | ||
+ | * 32 - omit DOC images | ||
+ | * 64 - omit multiple NQ image series | ||
+ | |||
+ | Downsampling by N means only 1 image is saved per N in list. | ||
+ | |||
+ | If NDAYS, only studies with scan_date less than NDAYS old (default=30). | ||
+ | |||
+ | ==== Mode 3 - copy local data to OUTDIR for qualifying studies ==== | ||
+ | For each qualifying study, copy BXH files to 4D format in new study dir | ||
+ | |||
+ | FLAG:\\ | ||
+ | * 1 - create WDF file (assumed if WDF specified) | ||
+ | * 2 - deidentify name,patid | ||
+ | * 4 - remove dates | ||
+ | * 8 - NDAYS is relative to last update in STUDYTABLE, instead of scan date | ||
+ | * 16 - don't include NQ axial (series 53) | ||
+ | * 32 - don't include DTI orig images | ||
+ | * 64 - include Result series 500-799 | ||
+ | * 128 - include float 800 series | ||
+ | * 256 - include integer 900 series | ||
+ | * 512 - include all NQ series | ||
+ | * 1024 - testing -- don't create/copy files | ||
+ | |||
+ | If NDAYS, only studies with scan_date (or update date) less than NDAYS old (default=30). | ||
+ | |||
+ | ==== Study table format: 1 row per scan session==== | ||
+ | Column description: | ||
+ | FLAG: | ||
+ | * 0 - study found, no series table yet | ||
+ | * 1 - study has been modified | ||
+ | * 2 - series table updated | ||
+ | * 3 - Local BXH file for each DICOM series | ||
+ | * 4 - Local WDF updated | ||
+ | * 8 - Images transferred to remote disk 4D BXH's | ||
+ | * 16 - Functional maps generated | ||
+ | * 32 - DTI tracking done | ||
+ | * 1024 - study in table but server data directory missing | ||
+ | * 2048 - study in table but scan name/ | ||
+ | |||
+ | ==== Series table format -- Created automatically for each study in Study Table ==== | ||
**See Also:**\\ | **See Also:**\\ |