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jvs:fscan:manual:chapter2:invivo [2013/08/12 16:33]
voyvodic
jvs:fscan:manual:chapter2:invivo [2014/08/04 16:03] (current)
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 ===== Table InVivo -- Special case InVivo data tables ===== ===== Table InVivo -- Special case InVivo data tables =====
 **usage:** **usage:**
- * **-table invivo ​TBLNAME ​NAME**\\ +  ​* -table invivo ​studytable ​studiesdir tbldir serage examage sernum 
- * **-table invivo ​TBLNAME ​NAME**\\ +  * -table invivo ​studytable ​studiesdir tbldir outdir flag [wdf] [ndays] [minseries] 
- * **-table invivo ​TBLNAME ​NAME**\\ +  * -table invivo ​studytable ​studiesdir tbldir outdir flag [wdf] [ndays] [minseries]
- * **-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'​s DynaSuite workstations. This command expects an existing table for its STUDYTABLE argument with a predefined structure (described below). For each separate study (row) in STUDYTABLE it will automatically create/​read/​modify an image series table (described below) unique to that study.
  
 +STUDYTABLE is the name of the data table being manipulated. In general this table should already exist (i.e., created by a previous [[jvs:​fscan:​manual:​chapter2:​table|Table]] command).
  
-The TABLE INVIVO command is used for manipulating ​tables ​associated ​with data files on an InVivo DynaSuite image processing systemThis is a special case addition to fScan'​s standard [[jvs:​fscan:​manual:​chapter2:​table|Table]] command+==== 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/​DCM-Input modified within last NDAYS. 
 +Find first DICOM file for each series to get patname, ID, date, time, etc fields
  
-TBLNAME is the name of the data table being manipulated. In general this table should already exist (i.e., created ​by a previous [[jvs:​fscan:​manual:​chapter2:​table|Table]] command).+==== 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 +FLAG: 
-  * 1 - make study table. Look for subdirs names Study#{...} in dir NAME +  * 1-7 - downsampling by this many images (default=5) 
-  * make series ​table. NAME is DCM dirlook for subdirs named Series{...} +  * downsample 500+ series ​lists if NIMGS > 50 
-  ​* ​3 - make dicom table. Look for .dcm files in dir NAME get zpostpos from each +  * 16 - downsample any DICOM series if NIMGS > 50 
-  * 4 - make imagedata table. Look for ImageData subdirs within dir NAM. Look for .data and .gvr files in each subdir +  * 32 - omit DOC images  
-  * create bxh file NAME from dicom table +  * 64 - omit multiple NQ image series 
-  * create bxh file's named NAME_num.bxh from imagedata ​table, where num is row num + 
-  * create wdf file NAME from series table +Downsampling by N means only 1 image is saved per N in list.  
-  * 8 - create/add wdf file NAME from imagedata ​table+ 
 +If NDAYSonly 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: 
 +  * 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/date/time info missing 
 + 
 +==== Series ​table format -- Created automatically for each study in Study Table ====
  
 **See Also:**\\ **See Also:**\\
jvs/fscan/manual/chapter2/invivo.1376325239.txt.gz · Last modified: 2014/08/04 16:03 (external edit)