Hi Paige,
Your operating system might report the output of concat_bvars as being
a .docx file, but it is actually an internal FSL format that you
cannot view/read directly.
Paul
On 04/06/2019, Elizabeth Paige <[log in to unmask]> wrote:
> 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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