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Hi Paul, This is the response I get when I type Fsl_prepare_fieldmap: Usage: FSl_prepare_fieldmap <scanner> <phase_image> <magnitude_image> <out_image> <deltaTE (in ms)> [--nocheck] Prepares a fieldmap suitable for FEAT from SIEMENS data - saves output in rad/s format <scanner> must be SIEMENS <magnitude image> should be Brain Extracted (with BET or otherwise) <deltaTE> is the echo time difference of the fieldmap sequence - find this out form the operator (defaults are *usually* 2.46ms on SIEMENS) --nocheck supresses automatic sanity checking of image size/range/dimensions e.g. FSl_prepare_fieldmap SIEMENS images_3_gre_field_mapping images_4_gre_field_mapping fmap_rads 2.65 Perhaps there was a spelling error before. However, doe this command only apply to fmri data? *Best regards,* *Isobel French* *Researcher and Coordinator* *Neurosurgery Research Unit, Division of Neurosurgery* *Department of Surgery, Faculty of Medicine* *University Malaya* *Suite 15 T8-4a * *Level 4, Menara Timur* *University of Malaya Medical Center* *016-7937605* *03-79493138* On Wed, Nov 9, 2016 at 5:07 PM, paul mccarthy <[log in to unmask]> wrote: > Hi Isobel, > > What happens when you type Fsl_prepare_fieldmap into a terminal? > > Paul > > On 9 November 2016 at 09:07, paul mccarthy <[log in to unmask]> > wrote: > >> Hi Isobel, >> >> What happens when you type FSL_preepare_fieldmap >> >> On 8 November 2016 at 02:29, Isobel French <[log in to unmask]> wrote: >> >>> Hi Paul, >>> >>> Where is the GUI Fsl_prepare_fieldmap located? I can't seem to find it >>> or open it from the terminal. >>> >>> Thanks. >>> >>> >>> *Best regards,* >>> >>> *Isobel French* >>> >>> *Researcher and Coordinator* >>> *Neurosurgery Research Unit, Division of Neurosurgery* >>> *Department of Surgery, Faculty of Medicine* >>> *University Malaya* >>> >>> *Suite 15 T8-4a * >>> *Level 4, Menara Timur* >>> *University of Malaya Medical Center* >>> >>> *016-7937605* >>> *03-79493138* >>> >>> On Mon, Nov 7, 2016 at 2:32 PM, Isobel French <[log in to unmask]> >>> wrote: >>> >>>> Hi Paul, >>>> >>>> Ok sure thanks. >>>> >>>> >>>> *Best regards,* >>>> >>>> *Isobel French* >>>> >>>> *Researcher and Coordinator* >>>> *Neurosurgery Research Unit, Division of Neurosurgery* >>>> *Department of Surgery, Faculty of Medicine* >>>> *University Malaya* >>>> >>>> *Suite 15 T8-4a * >>>> *Level 4, Menara Timur* >>>> *University of Malaya Medical Center* >>>> >>>> *016-7937605* >>>> *03-79493138* >>>> >>>> On Fri, Nov 4, 2016 at 5:17 PM, paul mccarthy <[log in to unmask]> >>>> wrote: >>>> >>>>> Hi Isobel, >>>>> >>>>> This is all covered in the user guide and the FSL course material - >>>>> refer to these for more information: >>>>> >>>>> - http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/BET/ >>>>> - http://fsl.fmrib.ox.ac.uk/fslcourse/lectures/practicals/r >>>>> egistration/index.html >>>>> >>>>> Cheers, >>>>> >>>>> Paul >>>>> >>>>> >>>>> >>>>> On 4 November 2016 at 02:29, Isobel French <[log in to unmask]> >>>>> wrote: >>>>> >>>>>> Hi Paul, >>>>>> >>>>>> The results turned out a little better but still not as desired. How >>>>>> do I go about manually tweaking the bet settings? >>>>>> >>>>>> Thanks. >>>>>> >>>>>> >>>>>> *Best regards,* >>>>>> >>>>>> *Isobel French* >>>>>> >>>>>> >>>>>>> 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, >>>>>>> >>>>>>> Paul >>>>>>> >>>>>>> On 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 1 >>>>>>>>>>>> >>>>>>>>>>>> Cheers, >>>>>>>>>>>> >>>>>>>>>>>> Paul >>>>>>>>>>>> >>>>>>>>>>>> On 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 1 >>>>>>>>>>>>> >>>>>>>>>>>>> Usage: 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, >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Paul >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> On 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, >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Paul >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> On 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 $FSLDIR >>>>>>>>>>>>>>>>>> yes/fsl >>>>>>>>>>>>>>>>>> [neuros-iMac-2:~] neuro% >>>>>>>>>>>>>>>>>> [neuros-iMac-2:~] neuro% flirt -version >>>>>>>>>>>>>>>>>> flirt: Command not found. >>>>>>>>>>>>>>>>>> [neuros-iMac-2:~] neuro% >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>> >>>>>>>>> >>>>>>>> >>>>>>> >>>>>> >>>>> >>>> >>> >> >