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Paul, Thank you! Also, when I do run the concat_bvars command, is it supposed to be a docx file? Because that’s what I’m getting every time. Thanks again Paige > On Jun 4, 2019, at 8:58 AM, paul mccarthy <[log in to unmask]> wrote: > > Hi Paige, > > Yes - the practical suggests that you set up your design using the Glm > gui, and then run first_utils after that. But at no point does it tell > you to select the .bvars file while setting up the design, so I'm not > sure why you're attemping to do this. All you should be doing is > defining your design matrix and contrasts. > > Cheers, > > Paul > > On 04/06/2019, Elizabeth Paige <[log in to unmask]> wrote: >> Hi Paul, >> I’m looking at the practical now and I’m very confused as to what to do to >> get the 4D nifty image. I see that the _first.bvars files come from FIRST, >> and that then I need to convert them into the nifty image, but I can’t find >> where it tells me how to do that. It does not mention first_utils until >> after the design matrix has been created. If you have time can you help me >> find this specifically? >> >> Thank you! >> Paige >> >>> On Jun 4, 2019, at 8:40 AM, paul mccarthy <[log in to unmask]> >>> wrote: >>> >>> Hi Paige, >>> >>> You must be skipping some steps - before you can run a higher level >>> analysis, you need to use first_utils to convert the .bvars file into >>> a 4D nifti image. This is all covered in detail in the practical. >>> >>> Cheers, >>> >>> Paul >>> >>> On 04/06/2019, Elizabeth Paige <[log in to unmask]> wrote: >>>> Hi Paul, >>>> Thank you for answering! I am using concat_bvars to prepare my >>>> segmentations, but I am getting the aforementioned error message when I >>>> try >>>> to load it to the gui, as I am told to do in the fsl course. >>>> Do you know why this error message is happening? >>>> Thank you! >>>> Paige >>>>> On Jun 4, 2019, at 4:17 AM, paul mccarthy <[log in to unmask]> >>>>> wrote: >>>>> >>>>> Hi Paige, >>>>> >>>>> concat_bvars is a preprocessing step needed to prepare sub-cortical >>>>> segmentations for a group analysis. >>>>> >>>>> I would recommend going through the FSL course material to familiarise >>>>> yourself with FSL - there is a good overview of the sub-cortical >>>>> analysis pipeline: >>>>> >>>>> http://fsl.fmrib.ox.ac.uk/fslcourse/ >>>>> http://fsl.fmrib.ox.ac.uk/fslcourse/lectures/practicals/seg_struc/index.html#first >>>>> >>>>> Cheers, >>>>> >>>>> Paul >>>>> >>>>> On 04/06/2019, Paige Oden <[log in to unmask]> wrote: >>>>>> Hello! I am very new to fsl and I am stuck. >>>>>> First, I'm not entirely sure what the output of concat is meant to be, >>>>>> but >>>>>> it keeps coming out as a document that will not open. The command line >>>>>> I'm >>>>>> using is: >>>>>> >>>>>> concat_bvars c_to_p_to_pdi_R_Hipp.bvars MJF*C_first_R_Hipp.bvars >>>>>> MJF*P_first_R_Hipp.bvars MJF*PCI_first_R_Hipp.bvars >>>>>> >>>>>> Definitely not sure if that's what I'm supposed to be using, or if >>>>>> that's >>>>>> what's supposed to be happening, but that's what it is. >>>>>> >>>>>> Furthermore, when I try to load this concatenated file into my Higher >>>>>> Level >>>>>> GLM gui, it says that "This" is an invalid command. I don't know what >>>>>> to >>>>>> do >>>>>> about this because I don't know where 'This' is coming from. >>>>>> >>>>>> Thank you! >>>>>> >>>>>> ######################################################################## >>>>>> >>>>>> To unsubscribe from the FSL list, click the following link: >>>>>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 >>>>>> >>>>> >>>>> ######################################################################## >>>>> >>>>> To unsubscribe from the FSL list, click the following link: >>>>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 >>>> >>>> ######################################################################## >>>> >>>> To unsubscribe from the FSL list, click the following link: >>>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 >>>> >>> >>> ######################################################################## >>> >>> To unsubscribe from the FSL list, click the following link: >>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 >> >> ######################################################################## >> >> To unsubscribe from the FSL list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 >> > > ######################################################################## > > To unsubscribe from the FSL list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 ######################################################################## To unsubscribe from the FSL list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1