jvs:fscan:manual:chapter2:invivo
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jvs:fscan:manual:chapter2:invivo [2013/08/12 16:33] – voyvodic | jvs:fscan:manual:chapter2:invivo [2014/03/24 16:59] – 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 performs customized manipulations on data tables describing MRI exam and scan data sets processed on InVivo' | ||
+ | STUDYTABLE is the name of the data table being manipulated. In general this table should already exist (i.e., created by a previous [[jvs: | ||
- | The TABLE INVIVO command is used for manipulating tables associated with data files on an InVivo DynaSuite image processing system. This is a special case addition | + | ==== Study table: 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 | ||
+ | * 16 - Functional maps generated | ||
+ | * 32 - DTI tracking done | ||
+ | * 1024 - study in table but server data directory missing | ||
+ | * 2048 - study in table but scan name/ | ||
- | TBLNAME is the name of the data table being manipulated. In general this table should already exist (i.e., created by a previous [[jvs: | + | ==== Series tables -- Created automatically for each study in Study Table ==== |
- | FLAG | + | ==== Mode 1 - find recently modified studies and update series tables ==== |
- | * 1 - make study table. | + | 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 |
- | * 4 - make imagedata table. Look for ImageData subdirs within dir NAM. Look for .data and .gvr files in each subdir | + | |
- | * 5 - create bxh file NAME from dicom table | + | ==== Mode 2 - create local BXH header files for each series |
- | * 6 - create bxh file's named NAME_num.bxh from imagedata table, where num is row num | + | For each series, created DICOM file table, |
- | * 7 - create wdf file NAME from series | + | |
- | * 8 - create/add wdf file NAME from imagedata table | + | ==== Mode 3 - copy local data to OUTDIR |
+ | For each qualifying study, copy BXH files to 4D format | ||
+ | |||
+ | FLAG:\\ | ||
+ | * 1 - create WDF file (assumed if WDF specified) | ||
+ | * 2 - deidentify name,patid | ||
+ | * 4 - remove dates | ||
+ | * 8 - don't include NQ axial (series 53) | ||
+ | * 16 - don't include DTI orig images | ||
+ | * 32 - include Result | ||
+ | * 64 - include float 800 series | ||
+ | * 128 - include integer 900 series | ||
+ | * 256 - include all NQ series | ||
+ | * 512 - testing -- don' | ||
**See Also:**\\ | **See Also:**\\ |
jvs/fscan/manual/chapter2/invivo.txt · Last modified: 2024/06/21 15:44 by 127.0.0.1