Prior to the adoption of the station and casts csv data processing formats in 2012. SIO-CalCOFI processed bottle data using the IEH-format developed in 1983 from the original CalCOFI SD2 data format. Fortran programs from a VMS mini-computer were ported to IBM PCs running DOS initially then updated to run under Windows. Each software transition was tested to insure the calculated data were identical - VMS vs DOS, DOS vs Windows, IEH vs Sta.csvs.
In order to bottle-correct CTD sensor data from cruises prior to the switch to sta.csvs in 2012, IEH files are required. Using SIO-CalCOFI authored software, BtlVsCTD.exe, this is done seamlessly but some additional checks are required.
This short list outlines those differences:

1. Use the cruise's "arch.ieh" file (YYMMarch.ieh such as 1004arch.ieh), not the "terpled" ieh (YYMMt.ieh ie 1004t.ieh). "Terpled" (interpolated) bottle data should not be used to bottle-correct CTD sensor data. Only actual bottle samples should be compared to CTD data.
2. "Arch.ieh" files should have sigma-theta and oxygen saturation in the optional "wildcard" columns (104-110). This originally required a DOS program Addstho2.exe to be run on the YYMMarch.ieh file(s). These two columns of calculated data are sometimes missing from archived ieh files so adding them prior to running BtlVsCTD is recommended in order to generate bottle oxygen data in uMol/kg.
3. When running BtlVsCTD.exe, be sure to checkbox "IEH" under "Bottle Data Source File" in the upper right on the main form. On the next form, be sure "yymmarch.ieh" is selected. This is the default setting but double-check and make sure the arch.ieh file is in the same CTD data directory. This will generate the merged CTD + bottle csv file that is imported into Excel for calculating the salt offsets and sensor regressions.
4. YYMMarch.ieh should be in the CTD data directory. Occasionally, downloaded IEH files are formatted without "line feed/caridge return" (ie DOS text format) and reads like one long line of text. This can be corrected with a text editor such as Ultradedit using the Unix/Mac to DOS text conversion. This is under menu "File/Conversion" in Ultraedit.
5. *2004 ISUS + 9 additional stations added: an ISUS nitrate sensor and 9 additional SCCOOs stations were added in 2004. Prior to these station additions, a typical CalCOFI cruise occupied 66 stations. Winter & Spring cruises can include more if the station pattern extends north of Pt Conception.
6. *Aug 2009: a new 911+ CTD & deck unit (v2) were purchased with new dual sensor arrays including dual O2 sensors - cruises prior to 0908 had dual T & C but only one O2 sensor. CalCOFI started using a version 2 deck unit, which automatically offsets the secondary conductivity sensor . Secondary conductivity sensor data from earlier cruises (1992-200407) require an offset of 0.073secs in AlignCTD. A SBE 18 pH sensor  was added to the sensor array in late 2009.

*BtlVsCTD should handle all sensor configurations and generate the same number of data columns regardless of sensors deployed or missing. The voltage channels for each sensor have been somewhat standardized on recent cruises. But sensors may be on different voltage channels depending on the sensor array deployed. Refer to the cast's .hdr, .con files, or cruise CTD summary for sensors used & their arrangement.

Seasoft Note: CalCOFI's Seabird CTD raw data from mid-1998 to present can be processed using Seasoft for Windows. The raw CTD data collected before Sept 1998 (9808 and earlier) require Seasoft for DOS. Seasoft for DOS will run on Windows XP, 7, or 10 computers using a DOS command line. Windows XP has a compatible DOS command executable that will run Seasoft for DOS. On Windows 7 or 10 computers, a DOS program called DOSBox can be used to run Seasoft for DOS. Seasoft for DOS is required to convert the raw CTD .dat files to .cnv, which can then be processed by Seasoft for Windows. DOSBox will also run Addstho2.exe which will add sigma-theta and oxygen saturation columns to IEH files.