Hi,

Open the ~/.bashrc file and paste this line into it:
. /etc/fsl/4.1/fsl.sh

Make sure, that you also copy the initial dot. To make this change effective, it will be best, if you logout first. After logging in again, the configuration should be read and everything should work, I hope.

There is no need to change the fsl.sh file, except you want to change the standard output type, or use parallel processing. The latter does not really make sense, if you run FSL locally in a virtual box.

It might be a good idea, to modify the settings in VirtualBox for your virtual machine, i.e. increase memory etc. However, be aware, that you do not have much memory, so depending on the analysis and data size, you might run into trouble. If this is the case, you might want to consider, to natively install Linux on your Laptop, and make it maybe Dual Boot, i.e. you decide when starting, whether you want to run Linux, or Windows (I assume) instead. Anyhow, increasing RAM is always a good idea.

Good luck,
wolf

On 01/31/2013 05:01 PM, Sandra Petris wrote:

Ok thanks. From the terminal I open with nano function the fsl.sh file....but dont know what to do now. do i have to add a line?

many thanks for your help!

ciao

sandra

ps i'm very bad in programing so sorry if i make silly questions

2013/1/31 wolf zinke <[log in to unmask]>

Hi,

If you source the configuration (in case of FSL 4.1 it is this line:. /etc/fsl/4.1/fsl.sh), then there should be no need for this prefix anymore. It is also important to source this configuration in order to set the environmental variables  for FSLOUTPUTTYPE and FSLDIR.


have fun,
wolf

On 01/31/2013 04:13 PM, Sandra Petris wrote:

Hi I found out all the fsl scripts in the usr/bin directory and the problem was....very silly it was a matter of writing: with this vm before writing any script you nedd to write fsl4.1 -.

So for example if you need to run the randomise script, you have to write the following:

fsl4.1-randomise.......

thanks for you help!!

sandra

2013/1/31 wolf zinke <[log in to unmask]>

Hi,

I think the more convenient way to install packages required for FSL is to use the Synaptic package manager (in the top panel in the system->Administration menu). Search in this GUI fo fsl and select all required packages. Make sure to have the atlases installed as well. (you also can run 'aptitude install fsl').

I am not sure, if you need to source the configuration script on NeuroDebian as well, if so, you have to add the following line to the ~/.bashrc file:. /etc/fsl/5.0/fsl.sh

Check also http://neuro.debian.net/debian/extracts/fsl/README.Debian

hope this helps,
wolf

On 01/31/2013 03:01 PM, Sandra Petris wrote:

Hi Wolf,

thanks for your help. I did install the vm (Virtual MAchine of NeuroDebian) following your suggestion and I downloaded fsl 4.1 (it was somehow preconfigured to dowload it). Even if I can open the gui from the terminal and visualize images with fslview, I cannot use the TBSS scripts (I need to run TBSS analysis). For example if I run the  " tbss_1_preproc *nii.gz" and I am in the folder where the Fa images are, the terminal says that the command is not found.......

do you know what might be going on?

thanks a lot

ciao

sandra

2013/1/31 wolf zinke <[log in to unmask]>

Hi,

Are you running Windows?

You can use the Virtual MAchine of NeuroDebian (http://neuro.debian.net/vm.html#chap-vm), which runs with Virtualbox.

Good luck,
wolf

On 01/31/2013 10:56 AM, Sandra Petris wrote:

Dear Fsl experts,

I have a lenovo Intel Pentium CPU B960 2.20 GHz and 4 GB of RAM with no virtualization technology supported therefore I cannot install the VMware Player and Fsl vm.....I'm quite desperate.. is there any other way to install fsl efficiently on this kind of PC or it is not powerful enough?

Thanks a lot and any advice will be greatly appreaciated

Cheers

sandra