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Hi thanks a lot for your help!. Does the attached Fa image look normal? thanks a lot cheers, sandra 2013/1/31 wolf zinke <[log in to unmask]> > 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 >>>>> >>>> >>> >>> >> >> > >