I still don't know what you mean. Can you try to explain more clearly please?
Saad
On 8 Apr 2013, at 17:35, Nucleos P wrote:
> Here was the suggestion:
>
> "The dyad1/PDD is a vector, so a 4D image with the 4th dimension ("volume" in FSLview) representing the x, y and z components of the PDD. So you need to vecreg the dyad1 using the TBSS warpfield and then take the absolute value of the 1st, 2nd and 3rd volume of the vector."
>
> On Mon, Apr 8, 2013 at 12:33 PM, Saad Jbabdi <[log in to unmask]> wrote:
> Sorry, I don't know what you mean...
>
> Cheers,
> Saad
>
>
> On 8 Apr 2013, at 17:28, Nucleos P wrote:
>
>> Hi Saad,
>>
>> Thank you very much for your suggestions. They have proven to be very helpful.
>>
>> How would I produce the values for the 1st, 2nd, and 3rd volume of the vector?
>>
>> Thanks,
>> Catherine
>> On Fri, Apr 5, 2013 at 4:11 PM, Saad Jbabdi <[log in to unmask]> wrote:
>> Hi
>> You can resample vector data using "vecreg", provided that you have a transformation that you got with either FLIRT or FNIRT. Vecreg allows you to apply this transformation to vector data (e.g. the dyads).
>>
>> If you want to average vector data across subjects (after registration), then you can use this tool: www.fmrib.ox.ac.uk/~saad/average_vectors
>>
>> If you want to extract the x y z components (not sure why you would want to do that), then you can use "fslroi".
>>
>> Cheers
>> Saad
>>
>>
>> On 5 Apr 2013, at 15:49, Nucleos P wrote:
>>
>>> Hello Saad -
>>>
>>> Okay - That's understandable about tbss. I really just need a way to
>>> register the images to the MNI152 template space.
>>>
>>> Is there a way register the subjects' dyads1* images to MNI152 space
>>> and then create x, y, z, vector component maps (e.g. Just x vector
>>> map, just y vector map, and just z vector map)?
>>>
>>> Thank you very much!
>>> -Catherine
>>>
>>> On 4/5/13, Saad Jbabdi <[log in to unmask]> wrote:
>>>> I don't think you can use the dyads in a tbss-style analysis. It makes more
>>>> sense for scalar data.
>>>>
>>>> Saad
>>>>
>>>>
>>>> On 5 Apr 2013, at 14:00, Nucleos P wrote:
>>>>
>>>>> Hi Saad,
>>>>>
>>>>> It is actually the map the dyads1* images not the FA map. FSL tbss just
>>>>> uses the same naming convention (~FA) for all inputs.
>>>>>
>>>>> Thanks,
>>>>> Catherine
>>>>>
>>>>>
>>>>>
>>>>> On Fri, Apr 5, 2013 at 5:10 AM, Saad Jbabdi <[log in to unmask]> wrote:
>>>>> Hi - sorry I don't understand what you're saying. FA is a scalar map, so
>>>>> there is no x,y,z component to it.
>>>>>
>>>>> Saad
>>>>>
>>>>>
>>>>>
>>>>> On 5 Apr 2013, at 00:03, Nucleos P wrote:
>>>>>
>>>>>> Hi Saad,
>>>>>>
>>>>>> I have used the fslroi tool to extract voxel masks with specific x,y,x
>>>>>> coordinates.
>>>>>>
>>>>>> To exclude the x and y vector maps to get the z vector map what
>>>>>> parameters would I choose?
>>>>>>
>>>>>> fslroi <input> <output> <xmin> <xsize> <ymin> <ysize> <zmin> <zsize>
>>>>>>
>>>>>> My input would be the all_FA.nii
>>>>>>
>>>>>> ...any suggestions?
>>>>>>
>>>>>> Thank you,
>>>>>> Catherine
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> On Thu, Apr 4, 2013 at 4:12 AM, Saad Jbabdi <[log in to unmask]> wrote:
>>>>>> Hi - you can use fslroi for this.
>>>>>>
>>>>>> Saad
>>>>>>
>>>>>> On 3 Apr 2013, at 22:58, Nucleos P wrote:
>>>>>>
>>>>>>> Hello experts -
>>>>>>>
>>>>>>> Would you happen to know any programs or scripts that could help create
>>>>>>> individual x, y, z vector maps from a primary eigenvector map?
>>>>>>>
>>>>>>> Currently, I use FSL and get both dyads1* output from the bedpostx and
>>>>>>> V1 output from dtifit.
>>>>>>>
>>>>>>>
>>>>>>> I would like to find a way to extract the 3 vector components from the
>>>>>>> maps.
>>>>>>>
>>>>>>>
>>>>>>> Thanks in advance for your time and help,
>>>>>>> Catherine
>>>>>>
>>>>>> --
>>>>>> Saad Jbabdi
>>>>>> University of Oxford, FMRIB Centre
>>>>>>
>>>>>> JR Hospital, Headington, OX3 9DU, UK
>>>>>> (+44)1865-222466 (fax 717)
>>>>>> www.ndcn.ox.ac.uk/team/researchers/saad-jbabdi
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>> --
>>>>> Saad Jbabdi
>>>>> University of Oxford, FMRIB Centre
>>>>>
>>>>> JR Hospital, Headington, OX3 9DU, UK
>>>>> (+44)1865-222466 (fax 717)
>>>>> www.ndcn.ox.ac.uk/team/researchers/saad-jbabdi
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>
>>>> --
>>>> Saad Jbabdi
>>>> University of Oxford, FMRIB Centre
>>>>
>>>> JR Hospital, Headington, OX3 9DU, UK
>>>> (+44)1865-222466 (fax 717)
>>>> www.ndcn.ox.ac.uk/team/researchers/saad-jbabdi
>>>>
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>>
>> --
>> Saad Jbabdi
>> University of Oxford, FMRIB Centre
>>
>> JR Hospital, Headington, OX3 9DU, UK
>> (+44)1865-222466 (fax 717)
>> www.ndcn.ox.ac.uk/team/researchers/saad-jbabdi
>>
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>
> --
> Saad Jbabdi
> University of Oxford, FMRIB Centre
>
> JR Hospital, Headington, OX3 9DU, UK
> (+44)1865-222466 (fax 717)
> www.ndcn.ox.ac.uk/team/researchers/saad-jbabdi
>
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--
Saad Jbabdi
University of Oxford, FMRIB Centre
JR Hospital, Headington, OX3 9DU, UK
(+44)1865-222466 (fax 717)
www.ndcn.ox.ac.uk/team/researchers/saad-jbabdi
