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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