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--- jvs:fscan:manual:chapter2:invivo [2013/08/12 16:33]
voyvodic
+++ jvs:fscan:manual:chapter2:invivo [2023/02/23 18:43] (current)
@@ Line 3: / Line 3: @@
 ===== Table InVivo -- Special case InVivo data tables =====
 **usage:**
- * **-table invivo TBLNAME 1 NAME**\\
+  * -table invivo studytable 1 studiesdir tbldir serage examage sernum
- * **-table invivo TBLNAME 2 NAME**\\
+  * -table invivo studytable 2 studiesdir tbldir outdir flag [wdf] [ndays] [minseries]
- * **-table invivo TBLNAME 3 NAME**\\
+  * -table invivo studytable 3 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 system. This 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)
-  * 2 - make series table. NAME is DCM dir, look for subdirs named Series{...}
+  * 8 - downsample 500+ series lists if NIMGS > 50
-  * 3 - make dicom table. Look for .dcm files in dir NAME get zpos, tpos 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
-  * 5 - create bxh file NAME from dicom table
+  * 64 - omit multiple NQ image series
-  * 6 - create bxh file's named NAME_num.bxh from imagedata table, where num is row num
-  * 7 - 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 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/date/time info missing
+==== Series table format -- Created automatically for each study in Study Table ====
 **See Also:**\\

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