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!
>>>>>
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