NVM Help
Files
Note: The User’s Prefix [seg prefix] is a short string (e.g. "rjm")
that is used as a prefix for file names so different operators can use the same
directories.
User’s Home Directory
- Preferences File .nvm_preferences.xml
This file contains preferences that modify the behavior of nvm. Note that the
first character is a period "." so that this file is hidden on unix
systems.
Project Directory
All files are tied to a particular project and should be stored in the same location
for easy backup and comprehensive documentation.
- Program Directory
- Object Code Directory: bin
Exact version of the executable code used for this project with all necessary
libraries statically linked
- Source Code Directory
- Help Directory
Contains NVM's html files
- SegMentor Directory
Any SegMentor scripts that are used for this project
- Default Label File defaultLabel.xml
This file has a list of names of the usual structures and their colors. Labels
can be applied to outlines and surfaces
- Nauty Guess File
- Scans Directory
- Images Directory
Path example: /Image/PID/SCN/PID_SCN_SLICE.img
- Data Directory
Path example: /Data/PID/SCN
- “info” file
This contains various types of information, including the location of the
image files that are associated with the data in this directory.
- Outline Directory and files: otl/[seg prefix]nvmUserLog# (where
# is the date (YYYYMMDDHHMMSS)
example: rjm30.otl for slice 30
This is an "outline" file. It is in "gdf" format and
consists mainly of a list of points (x,y) and a label which designate the
border of a neuroanatomical structure in a particular slice of a scan.
- Log Directory and files: log/[seg prefix]#.otl
- Volume File [seg prefix]_Volume.csv
A comma separated value text file that can be imported into a spreadsheet.
- Landmark File [seg prefix]_Landmark.xml
This file contains a list of 3D locations and their labels
- Contour file [seg prefix]_contour.buchar (and .hdr)
This pair of files is the raw image data that represents contours. The number
of columns, rows, and slices is given in the .hdr file and "buchar"
indicates that each voxel is saved as a binary character (8 bits). Each
bit represents a different contour
- AutoContour file [seg prefix]_AutoContour.xml
This file holds the data for the AutoContour feature of nvm. It consists
mainly of a value for each slice.
- Final Results Directory
Archive Directory
- On Site
This should be located on a separate disk and computer from the above files.
- Off Site Duplicate