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!
>>>>>>
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