BrainSaw FAQ

Problems and solutions to common issues

Analysis

Where is stuff mounted?

The acquisition PCs are all in /mnt/ e.g. /mnt/brainsaw The data land on /mnt/data/BakingtrayStacks/ Ceph mount points are in /mnt/ceph

It didn't stitch

Check that all the data are present on joiner:

cd /mnt/data/BakingtrayStacks/MySample

If you see a file called FINISHED then all the data are copied from the acquisition PC to joiner. If not, you should rsync it over. If there is no 'stitchedImages_100folder then it didn't start stitching. If there is nodownsampled_stacks` folder then it didn't finish stitching or did not generated the downsampled stacks. You can stitch (including stitching only missing sections) and downsample by doing (in MATLAB):

stitchAllChannels; downsampleAllChannels(25)

from the sample directory.