It is possible to encounter this error message particularly if trying to open a large number of DICOM images. In most cases, each slice in a DICOM series is stored in an individual file; all of these files must remain open while the image is loaded. In addition, the maximum number of files open at any time (imposed by the kernel, not MRtrix3) may be relatively small (e.g. 256), such that very few subjects can be opened at once.
There are two ways to solve this issue:
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Reduce the number of files opened concurrently: By converting each series of interest to an alternative format (e.g. MRtrix image formats) before opening them in
mrview, the total number of files open at once will be drastically reduced. -
Increase the limit on number of files opened: If directly opening DICOM images without first converting them is more convenient, then it is possible to instead increase the kernel’s upper limit on the number of files that can remain open at once. The specific details on how this is done may vary between different OS’s / distributions, but here are a couple of suggestions to try:
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The current limit should be reported by:
ulimit -n -
Try running the following (potentially with the use of “
sudo”):sysctl -w fs.file-max=100000If this solves the issue, the change can be made permanent by editing file
/etc/sysctl.conf, adding the following line (replacing “<number>” with your desired upper limit):fs.file-max = <number>On MacOSX, you may instead need to look at the “
kern.maxfiles” and “kern.maxfilesperproc” parameters. -
Set the new upper limit using “
ulimit” (you can try using a number instead of “unlimited” if you choose to):ulimit -n unlimitedIf this works, you will need to add that line to a file such as “
~/.bashrc” in order for the change to be applied permanently.
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