Frequently Asked Questions

Starting Jim

  • Q. How can I make Jim start up in a particular directory?

A. The startup directory (folder) for Jim can be set in the user preferences. Select Preferences from the Jim's Toolkits menu, then the Misc tab, and set the new startup directory by pressing the startup_folder_button button.

On Unix systems (including Mac OS), you may also supply the name of the image file or directory as an argument when you start Jim from the command line.

  • Q. On a Unix system I see the error message: ** Line too long.
    when I run the stand-alone tools. What can I do?**

A. This means that your PATH environment variable is too long. You need to shorten it by editing your .cshrc file.

Converting Images

  • Q. My images are not in UNC, AnalyzeTM, NIFTI or DICOM format, nor are they in one of the import formats. Can I use Jim?

A. If your images are in a binary format with all pixel values in one slice contiguous within the file, then you will probably be able to use the Raw Converter to read your image data. If this is not the case, or if you are experiencing problems reading your data, contact Xinapse Systems at support to discuss your requirements. We will probably be able to include your image file format into the capabilities of Jim.

  • Q. My images are in DICOM format, but Jim doesn't put them in the image tree when I try to Import or Convert them. What's going wrong?

A. Jim recognises most DICOM and ACR-NEMA file formats, but there are many variants on image compression, as well as proprietary "encapsulated" file formats. Contact Xinapse Systems at support so that we can ensure that Jim will read your particular variant.

Loading Images

  • Q. Does Jim support AnalyzeTM lookup tables for colour mapping?

A. Yes. If there is a file with extension ".lkup" with the same name as the image file, then Jim will automatically load the colour lookup table.

  • Q. How does Jim recognise the different types of image file?

A. UNC images are recognised by the "Magic Number" at the start of the file: the first 8 bytes of the file are always 0x00000075000000FF. AnalyzeTM files are recognised by the extension of the header file (.hdr or .hdr.gz). NIFTI images are recognised by the extension of the header file (.hdr, .nii, .hdr.gz or .nii.gz). DICOM files and files that can be loaded or imported are recognised by attempting to parse the file contents.

If you have any queries about Jim, mail to support so that they can be added to this FAQ.