Appendix A: MRC to Analyze

This appendix will describe the process of converting MRC files into Analyze files. Two methods of accomplishing this are presented: one for individual files, the second for batch conversions of multiple files.

In this appendix, Analyze_AVW refers to Analyze_AVW version 2.5 (also known as Analyze_PC 2.5 on Windows NT systems). Analyze (without the AVW) refers to Analyze 7.5, the now outdated version of Analyze that saved files using the filename.hdr and filename.img extensions. Note the difference in nomenclature from the rest of this technical report.

This page uses the sample dataset glurigor.mrc, available as hyperlinked. This help page also makes use of several Suprim programs for analyzing and converting the files. Suprim is available for AIX and IRIX systems from http://www.itg.uiuc.edu/resources/suprim/.

Converting Individual MRC Files

It is assumed that the MRC file has a 1024 byte header at the top of the file containing information about the dimensions and type of data contained.

1. If the dimensions of the data are known, skip to the next step. Otherwise use the showmrc or hdim program that comes with Suprim. For example:

   sgi> showmrc < glurigor.mrc
   Number of columns, rows, sections ........ 73 101 101
   Map mode ................................. 2
   Start points on columns, rows, sections .. 0 0 0
   Grid sampling on x, y, z ................. 73 101 101
   Cell dimensions .......................... 73.0 101.0 101.0
   Cell angles .............................. 90.0  90.0  90.0
   Fast, medium, slow axes .................. X Y Z
   Origin on x, y ........................... 0.000000 0.000000
   Minimum density .......................... -29.000000
   Maximum density .......................... 58.000000
   Mean density ............................. 14.500000

   or

   sgi> hdim < glurigor.mrc
   -x   73 -y  101 -z  101 -w    0

2. Start Analyze_AVW, and launch the File:Import/Export... tool. Choose Tools:Raw Data... from the ImportExport 2.5 applet menu bar.
3. Press the File button and select the file.
4. Modify the following fields to match the dimensions and data type of your MRC file. Based on the glurigor.mrc example above:

   	Field	Value
   Input	Byte Offset	1024
   	once per	file
   	Width	101
   	Height	101
   	Depth	73
   	Volumes	1
   	Data Type	Float
   Output	File	glurigor.avw
   	File Format	AnalyzeAVW

5. Press Display. The Range, Scale Max and Scale Min fields should now adjust themselves to what is actually contained in the data. This is a bug in Analyze_AVW: the Display button must be pressed first. If not, an "Incompatible Image" error message will be generated.
6. Press Convert. The file will now be converted into the Analyze_AVW format, and can be loaded onto the Analyze_AVW desktop for further manipulation.

Batch Conversion To Analyze Format

MRC files can be converted into Analyze 7.5 format (e.g. glurigor.hdr, glurigor.img) using a combination of scripts, Analyze "extras", and Suprim programs. See the Suprim homepage for information about how to obtain Suprim. The Analyze program make_hdr was distributed with the Analyze 7.5 distribution and is not available for download from the ITG website. Contact the Biomedical Imaging Resource directly for further information about purchasing a copy.

The PERL script mrc2an may be downloaded from this website, but is already installed on all ITG systems. If downloading to another system, edit the mrc2an file changing the following lines:

Once installed, type mrc2an at the command line, adding the -b option if the dataset must be converted from floating point to bytes, followed by a list of MRC file names in order to begin the conversion process:

sgi> mrc2an -b -d glurigor.mrc
Converting glurigor.mrc into /var/tmp/aaaa000xz byte format.
        /usr/local/bin/ftob < glurigor.mrc | \
            /usr/local/bin/tomrc > /var/tmp/aaaa000xz
Converting /var/tmp/aaaa000xz to glurigor.{hdr,img}
        DIMS: 73 101 101
        MIN: 0.000000
        MAX: 255.000000
        MODE: CHAR
        /usr/local/bin/hcut < /var/tmp/aaaa000xz \
            2> /dev/null > glurigor.img
        /usr/local/bin/make_hdr glurigor.hdr 73 101 101 \
            1 CHAR 255.000000 0.000000

mrc2an converted the file glurigor.mrc to glurigor.img and glurigor.hdr, suitable for reading into Analyze 7.5 or Analyze_AVW. It pulled the dimensions, minimum and maximum values, and data type from the MRC file, and stored that information into the Analyze header. The -d option simply turned on debugging information.

For more information on the mrc2an script, read the manpage either online here, or by installing the nroff source and typing man mrc2an at the command prompt.

Batch Conversion to Analyze_AVW Format

Batch conversion from the MRC format directly into the AVW format is still being worked on. In the meantime, use the conversion program mrc2an described in the previous section to convert the data to Analyze 7.5 format. Analyze_AVW will read Analyze 7.5 data files.

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