Try using the robustfov command on your images before running bet. If you still do not get good results, you will need to manually tweak the bet settings.Cheers,PaulOn 2 November 2016 at 04:30, Isobel French <[log in to unmask]> wrote:Hi Paul,Do you know-how I can use fslmaths to correct the results on bet? Some of the images I obtained do not give a whole brain.4 AM, Isobel French <[log in to unmask]> wrote:I see. Tqvm.On Thu, Oct 27, 2016 at 4:42 PM, paul mccarthy <[log in to unmask]> wrote:Hi Isobel,
Those two commands are identical, just with different file names
Cheers,
Paul
On 27 Oct 2016 03:16, "Isobel French" <[log in to unmask]> wrote:Dear Paul,I see. But why does the practical say to use the command fslroi dwidata nodif 0 1 then?Thanks.On Wed, Oct 26, 2016 at 6:53 PM, paul mccarthy <[log in to unmask]> wrote:Hi Isobel,Are you just trying to extract the first 3D volume of a 4D image? In that case, use fslroi as follows:fslroi data first_volume 0 1Cheers,PaulOn 26 October 2016 at 05:10, Isobel French <[log in to unmask]> wrote:Hi Paul,I tried carrying out fslroi on an eddy corrected dti data, and the response below was what I got:[neuros-iMac-2:YEOH_LE/3775/0] neuro% fslroi data 0 1Usage: fslroi <input> <output> <xmin> <xsize> <ymin> <ysize> <zmin> <zsize>fslroi <input> <output> <tmin> <tsize>fslroi <input> <output> <xmin> <xsize> <ymin> <ysize> <zmin> <zsize> <tmin> <tsize>Note: indexing (in both time and space) starts with 0 not 1! Inputting -1 for a size will set it to the full image extent for that dimension.[neuros-iMac-2:YEOH_LE/3775/0] neuro%What does this mean?Thanks.On Thu, Oct 6, 2016 at 1:09 PM, Isobel French <[log in to unmask]> wrote:Hi Paul,I did what you suggested and it is working. TQvm indeed!On Wed, Oct 5, 2016 at 5:03 PM, paul mccarthy <[log in to unmask]> wrote:Hi Isobel,It seems like there is something already in the default install location (/usr/local/fsl) - maybe a partial (failed) installation.Could you check the contents of /usr/loca/ (with "ls -l") ? If there is already an FSL installation in /usr/local/fsl, remove it and try installing again.Cheers,PaulOn 4 October 2016 at 10:45, Isobel French <[log in to unmask]> wrote:Hi Paul,I did what you suggested and this is what I got:Downloading FSL version 5.0.9 (this may take some time)Checking download...[OK] Download is good.Password:Password:Installing FSL software...[FAILED] "The contents of /usr/local doesn't look like an FSL installtion - will not install here, aborting install" ;[neuros-iMac-2:~/Downloads] neuro%What does this mean?On Fri, Sep 30, 2016 at 7:04 PM, paul mccarthy <[log in to unmask]> wrote:Hi Isobel,As a guess, it looks like one of the questions asked by the fslinstaller.py script was given an incorrect answer (e.g. 'yes' where there should have been a directory, or no answer [i.e. just press enter]).I would recommend that you try to run the installer script again.Cheers,PaulOn 30 September 2016 at 04:26, Isobel French <[log in to unmask]> wrote:Hi,After running the installer script I ran the command echo $FSLDIR and got the following as attached. What should I do now?Tqvm.[neuros-iMac-2:~] neuro% echo $FSLDIRyes/fsl[neuros-iMac-2:~] neuro%[neuros-iMac-2:~] neuro% flirt -versionflirt: Command not found.[neuros-iMac-2:~] neuro%