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FSL  April 2013

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Subject:

Re: X Y Z vector maps

From:

Nucleos P <[log in to unmask]>

Reply-To:

FSL - FMRIB's Software Library <[log in to unmask]>

Date:

Mon, 8 Apr 2013 15:48:51 -0400

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (314 lines)

Hi Saad,

Thank you, I will try this.

-Catherine

On 4/8/13, Saad Jbabdi <[log in to unmask]> wrote:
> Ok - then you can extract the xyz components using fslroi like this:
> 	fslroi PDD X 0 1
> 	fslroi PDD Y 1 1
> 	fslroi PDD Z 2 1
>
> saad
>
>
>
> On 8 Apr 2013, at 20:11, Nucleos P wrote:
>
>> We would like to see if there are similarities or differences among groups
>> in direction of primary diffusion in ROI. For instance, in the same ROI in
>> controls versus patients is there a difference in the directin of primary
>> diffusion (e.g. PDD=X in HC and PDD=Y in patients).
>>
>> Does that make sense?
>>
>> On Mon, Apr 8, 2013 at 12:37 PM, Saad Jbabdi <[log in to unmask]> wrote:
>> 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
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>
>>>> --
>>>> 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
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>
> --
> 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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