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jvs:fscan:manual:chapter2:invivo
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jvs:fscan:manual:chapter2:invivo [2014/03/24 17:00] voyvodic |
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| - | **fScan Reference Manual, Chapter 2 (CmdLineOptions): | ||
| - | ===== Table InVivo -- Special case InVivo data tables ===== | ||
| - | **usage:** | ||
| - | * -table invivo studytable 1 studiesdir tbldir serage examage sernum | ||
| - | * -table invivo studytable 2 studiesdir tbldir outdir flag [wdf] [ndays] [minseries] | ||
| - | * -table invivo studytable 3 studiesdir tbldir outdir flag [wdf] [ndays] [minseries] | ||
| - | |||
| - | 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: | ||
| - | |||
| - | ==== 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. | ||
| - | |||
| - | ==== 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 - don't include NQ axial (series 53) | ||
| - | * 16 - don't include DTI orig images | ||
| - | * 32 - include Result series 500-799 | ||
| - | * 64 - include float 800 series | ||
| - | * 128 - include integer 900 series | ||
| - | * 256 - include all NQ series | ||
| - | * 512 - testing -- don't create/copy files | ||
| - | |||
| - | ==== 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:**\\ | ||
| - | [[jvs: | ||
| - | |||
| - | [[jvs: | ||
| - | [[jvs: | ||
| - | [[jvs: | ||
| - | [[jvs: | ||
jvs/fscan/manual/chapter2/invivo.txt · Last modified: 2023/02/23 18:43 (external edit)
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