Dear Mark
I have been running fast for 122 images, and was successful for the first 70 images with this command: /usr/local/fsl/bin/fast -t 1 -n 3 -H 0.1 -I 4 -l 20.0 -b -o *_structural_averaged_brain *_structural_averaged_brain
This was initially obtained from running FAST with GUI and I was able to obtain each tissue volume for all 70. However, for the remaining 52 images using the same command I have encoutered a problem. While each partial volume image for each class has been created, I cannot extract the tissue volumes, instead I get an error that the image couldn't be opened. I then did a random check with fslview, and noticed that although each partial volume image has been created, and they all look good, they are all created in greyscale. So I thought that might be the reason, each tissue type cannot be differentiated from others. I then colour coded them with pve_0 as Green, pve_1 as Blue-Lightblue and pve_2 as Red-Yellow, and saved them. I thought that would do the trick, but when I run them I still get the same error. So I realised that my solution was perhaps too simplistic and there might something really wrong. I do not know what it is, and am not sure why it suddenly occurred from the 71st image onwards, which suggests to me at least something systematic. What could be the problem?
Thank you for your help
Best wishes
Zola
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