Hi

I think you're using an old version of FSL. The most recent version is 5.0.6. You can tell which version you're using by typing:

fsl

in the terminal and reading from the top of the GUI.

The file you're describing is distributed in FSL version 5. I looked in an old version on our server and it looks like that file was distributed by mistake. It doesn't have a size and I'm pretty sure the file JHU-ICBM-labels-2mm.nii.gz (or 1mm) is the one you're looking for.

Kx

On 9 February 2014 23:42, Ran Xu <[log in to unmask]> wrote:

Hi Kristie,

Thank you very much! I tried your command, and there is an error saying "Missing header/image file". I don't have this data "JHU-ICBM-labels-2mm.nii.gz" under $FSLDIR/data/atlases/JHU/, instead I have  "JHU-ICBM-WhiteMatter-labels-2mm.nii.gz" and this one can't be loaded in fslview. Under this directory I can open the rest files. 

You opened "JHU-ICBM-labels-2mm.nii.gz", is this in the new released atlas? 

Thanks again,

Ran

On Sun, Feb 9, 2014 at 2:28 PM, Kirstie Whitaker <[log in to unmask]> wrote:

I just tried running this command:

fslview $FSLDIR/data/atlases/JHU/JHU-ICBM-labels-2mm.nii.gz

and the file opened in fslview. Can you try the same command and let me know what error message is printed to the terminal or to the screen?

Kx

On 9 February 2014 20:22, Ran Xu <[log in to unmask]> wrote:

Hi Kristie,

Thanks for your reply. I am sorry I didn't express myself clearly. The problem is I can't open "JHU-ICBM-WhiteMatter-labels-2mm.nii.gz" using fslview. So I try to unzip it and use other software to open it, but I failed .

I also searched the FSL forum and others seemed to meet this problem before.

So I am wondering how to get the "JHU-ICBM-WhiteMatter-labels-2mm.nii.gz" that I can use?

Thanks a lot,

Ran

On Sun, Feb 9, 2014 at 1:01 PM, Kirstie Whitaker <[log in to unmask]> wrote:

Can you send the exact command that you're using? It may be that you aren't able to unzip to that location. Have you tried copying the file to one of your own directories and then unzipping it?

Another point is to consider why you need to unzip the file? Most FSL tools will allow you to work with it as a nii.gz file.

Kx

On 9 February 2014 18:50, Ran Xu <[log in to unmask]> wrote:

Dear FSL experts,

I can't unzip the JHU-ICBM-WhiteMatter-labels-2mm.nii.gz in FSL because it's broken, where can I download this data with nii format? My FSL version is 5.0 and this file still can't work. I also contacted the MRI_Studio and nobody responded.

Any advice will be appreciated.

Ran

--

Kirstie Whitaker, PhD
Research Associate

Department of Psychiatry
University of Cambridge

Mailing Address
Douglas House
18b Trumpington Road
Cambridge, CB2 8AH

Phone: +44 7583 535 307

Website: www.kirstiewhitaker.com

--

Kirstie Whitaker, PhD
Research Associate

Department of Psychiatry
University of Cambridge

Mailing Address
Douglas House
18b Trumpington Road
Cambridge, CB2 8AH

Phone: +44 7583 535 307

Website: www.kirstiewhitaker.com

--

Kirstie Whitaker, PhD
Research Associate

Department of Psychiatry
University of Cambridge

Mailing Address
Douglas House
18b Trumpington Road
Cambridge, CB2 8AH

Phone: +44 7583 535 307

Website: www.kirstiewhitaker.com