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Dear Mark,

What can I do to speed up the process if the files are taking too long to download? Thanks.

Best regards,

Isobel French
Academic Coordinator and Research Officer
Division of Neurosurgery
Department of Surgery
Faculty of Medicine
University of Malaya
016-7937605
03-79493138


On Mon, Dec 2, 2013 at 5:28 PM, Mark Jenkinson <[log in to unmask]> wrote:
Yes,
Mark


On 28 Nov 2013, at 09:47, Isobel French <[log in to unmask]> wrote:

Dear Mark,

Are you referring to the data files listed from number 1-5 ? Thanks a lot.

Best regards,

Isobel French

On Thu, Nov 28, 2013 at 5:41 PM, Mark Jenkinson <[log in to unmask]> wrote:
Hi,

You need to install the data first.
Read the FSL Course website carefully and it will explain what to do.

All the best,
Mark


On 28 Nov 2013, at 09:34, Isobel French <[log in to unmask]>
 wrote:

Dear Mark, 

When I list this:

cd ~/fsl_course_data/fdt/subj1
The answer i get is this:No such file or directory
What does this mean and what should i do? Thanks a million.

Best regards,

Isobel French
Academic Coordinator and Research Officer
Division of Neurosurgery
Department of Surgery
Faculty of Medicine
University of Malaya
016-7937605
03-79493138


On Thu, Nov 28, 2013 at 5:30 PM, Isobel French <[log in to unmask]> wrote:
Dear Mark,

Tq so much for letting me know. i am actually using FSL 5.0.2.2 and it took so ever a long time to actually be able to run and install it. would there be any website where i could learn scripting in order to run this software as well? Tqvm.

Best regards,

Isobel French
Academic Coordinator and Research Officer
Division of Neurosurgery
Department of Surgery
Faculty of Medicine
University of Malaya
016-7937605
03-79493138


On Thu, Nov 28, 2013 at 5:21 PM, Mark Jenkinson <[log in to unmask]> wrote:
Hi,

That is not the FSL Course practical, but old documentation (for FSL version 4).
New documentation is at:
And the FSL Course is at:
with the FDT practical at:

I am hoping that you are using FSL version 5 now (currently version is 5.0.5), as we do not recommend using an older version.

All the best,
Mark



On 28 Nov 2013, at 09:11, Isobel French <[log in to unmask]>
 wrote:

Dear Mark,

i actually want to run probabilistic tractography on the MRI scans that I have. This means that I would first have to do BET, and then FDt before I go through Probtracking right? Please advise. Tqvm. Btw, is this the link for the practical FSL course covering FDT? 


Tqvm


Best regards,

Isobel French
Academic Coordinator and Research Officer
Division of Neurosurgery
Department of Surgery
Faculty of Medicine
University of Malaya
016-7937605
03-79493138


On Thu, Nov 28, 2013 at 4:44 PM, Mark Jenkinson <[log in to unmask]> wrote:
Dear Isobel,

I do not understand what you are trying to do.
It is not necessary to run BET on your entire diffusion timeseries.
It is certainly not necessary to move things into standard space before running BET.

I would advise you to look at the practical in the FSL Course that covers FDT, as I think this will help you to understand the process better.

All the best,
Mark



On 28 Nov 2013, at 05:46, Isobel French <[log in to unmask]> wrote:

Dear All,

I have recently and successfully been able to run the BET on a Niftii file. The next step I will need to take is run the BET file through FDT n BEDPOSTx. However to do this I would need to change these files into the MNi space first, is that correct? In FDT when I try to run the file through BEDPOSTx it says file notofund in director. What does this mean? Does it mean that the file is not compatible with the software, or does it mean that the file cannot be located? I would just like to know, what would be the procedures to run the file through FDT? I am very new with this software. Your patience and guidance would be very much appreciated. Tqvm


Best regards,

Isobel French
Academic Coordinator and Research Officer
Division of Neurosurgery
Department of Surgery
Faculty of Medicine
University of Malaya
016-7937605
03-79493138