Dear Mark

Thank you for your response. I have checked dik space and that doesn't seem to be a problem. We have used 78% of space so far, with 389G available. 
The actual error is for each tissuetype is : Image Exception : #22 :: ERROR: Could not open image *_structural_averaged_brain_pve_*. 
I didn't create a directory to run FAST, so it was run in each individual subject file. I din't think this could cause a problem. When I run ls -l in each file, the permission rights are the same. 

I hope that helps?

Best wishes
Zola



________________________________________
From: FSL - FMRIB's Software Library [[log in to unmask]] on behalf of Mark Jenkinson [[log in to unmask]]
Sent: 07 February 2013 22:27
To: [log in to unmask]
Subject: Re: [FSL] FAST errors

Dear Zola,

It is very difficult to diagnose from this what might be the problem.
The images do not have colour embedded in them - this is purely added by the display tool.
So that doesn't explain it at all.

It could be a problem with your disk space or quota if it only occurred after a certain point and was consistent from that point onwards.  I would check that.

If this is not the problem, let us know the exact error you get when trying to calculate the volume.
And it would also be useful to know what the result of "ls -l" is when run on the file.

All the best,
        Mark



On 7 Feb 2013, at 13:07, Zola Mannie <[log in to unmask]> wrote:

> 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