I'm not sure I get you.
Do you want to go from a point in subject specific space to a point in
standard space?
J
On 13 Dec 2010, at 16:56, Erick Canales Rodriguez (Benito Menni CASM)
wrote:
> Hi Matt and Jesper,
>
> I'm really going to use the FNIRT method to transform the spatial
> points that belong to specific white matter tracts (computed by
> deterministic tractography) from the native space (diffusion MRI
> data) to the MNI space.
>
> The “fnirtfileutils” script allows computing the displacement field
> from the coefficients of the registration, which is evaluated by
> default in a 3D grid defined by the reference image.
> It is possible to compute (from the coefficients of the
> registration) the displacement field corresponding to a single point
> (or set of points) which coordinates are different to the
> coordinates defining the 3D grid (for example, a point defined in
> the continuous space not discrete)?
>
> A simple solution is to find the voxel containing the point of
> interest and then applying the displacement field associated with
> that voxel to the point of interest. However, this simple approach
> is not fine … There is any way to make this calculation more
> accurately with FSL tools?
> Thanks again,
> Regards,
>
> Erick J. Canales-Rodríguez
>
> (+34) 93 652 99 99 ext. 255
>
> Unitat de Recerca, Benito Menni CASM (http://www.hospitalbenitomenni.org/Default.aspx
> )
> Sant Boi del Llobregat (Barcelona), Espanya/España/Spain
>
> Benito Menni Complex assistencial en Salut Mental
> ________________________________________
>
> De: FSL - FMRIB's Software Library [[log in to unmask]] En nombre de
> Matt Glasser [[log in to unmask]]
> Enviado el: lunes, 13 de diciembre de 2010 16:17
> Para: [log in to unmask]
> Asunto: Re: [FSL] Advanced normalization options with FNIRT
>
> If you really want highly accurate registration of cortical grey
> matter, you
> are going to need to do something surface-based. Volume
> registration is not
> going to cut it. FNIRT is very good at aligning subcortical grey
> structures
> and white matter; however, the cortex has too much individual
> variability
> and needs to be registered in a way to respects its topology.
>
> Peace,
>
> Matt.
>
> -----Original Message-----
> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On
> Behalf
> Of Jesper Andersson
> Sent: Monday, December 13, 2010 6:27 AM
> To: [log in to unmask]
> Subject: Re: [FSL] Advanced normalization options with FNIRT
>
> Dear Erick,
>
>> In your opinion a computer (Linux) with 8 cores and 16 GB (or 24 GB)
>> of ram memory is sufficient to perform the registration using for
>> example a warp resolution of 5mm?
>>
>> The registration errors in the cortex, expected from a warp
>> resolution of 5mm, are in the range 1-2.5 mm?
>
> I am afraid it is not that simple. Firstly it is very hard to
> establish actual registration errors for non-linear registration since
> this is something that differ from voxel to voxel and for which one
> would need to know the ground truth for each voxel.
>
> What I have been able to do is to use a data set with manually
> delineated cortical regions for a number of subjects. I have then
> registered these subjects scans to each other and looked at how well
> the manually defined regions have aligned/overlapped. What I find from
> that is that there are large improvements in overlap (~between 50 to a
> 100% increases) when going from an affine transform to 10mm fnirt.
> When comparing 2mm fnirt to 10mm fnirt I find only marginal
> improvements in this population of normal subjects (this is the NIREP
> data set).
>
> I I was to venture a guess as to what that might mean in reduction of
> voxel-wise registration error I would guess maybe 0.5-1mm.
>
> I.e. you will not obtain a halving of the registration errors by
> halving the knot-spacing, but rather you will achieve a modest
> improvement.
>
>>
>> Thanks again for your comments and your excellent tool!
>
> Cheers!
>
> Jesper
>
>
>>
>> Erick
>>
>>
>> ________________________________________
>> De: FSL - FMRIB's Software Library [[log in to unmask]] En nombre de
>> Jesper Andersson [[log in to unmask]]
>> Enviado el: lunes, 13 de diciembre de 2010 11:36
>> Para: [log in to unmask]
>> Asunto: Re: [FSL] Advanced normalization options with FNIRT
>>
>> Dear Erick,
>>
>> The limitations to the resolution obtainable with the current version
>> of fnirt is not so much execution time as it is memory demands. I
>> think realistically that you cannot obtain a higher warp resolution
>> than 5mm, and even then you will need a powerful computer with a lot
>> of memory.
>>
>> That does not mean you cannot register your images to a template with
>> higher resolution than that. You can use the warp fields you obtain
>> from the "standard" fnirt registration to resample your images into
>> MNI 1mm or 0.5mm space by specifying one of those as the --ref
>> argument to applywarp. It should also be noted that a warp resolution
>> (knot spacing) of 10mm (the standard) does not imply a 10mm
>> registration error. My guesstimate is that registration errors in the
>> cortex are in the range 2-5mm, and less for central structures.
>>
>> The next version of fnirt will have the ability use a warp resolution
>> down to 1mm with reasonable memory requirements. When testing this
>> version I have found marginal advantages with 1mm over and above 10mm
>> for normal healthy subjects. The big difference, and benefit, is
>> mainly evident for elderly atrophied brains.
>>
>> Jesper
>>
>> On 13 Dec 2010, at 10:21, Erick Canales Rodriguez (Benito Menni CASM)
>> wrote:
>>
>>> Dear FSL experts,
>>>
>>> By default FNIRT was designed to be a "medium resolution" method
>>> that provides an excellent tradeoff between the accuracy of the non-
>>> linear registration and execution time (and working memory).
>>> However, my main interest is to apply the non-linear registration as
>>> accurate as possible - the execution time per subject is not a
>>> problem for my application. I am willing to wait as long as needed
>>> (within an interval of 24 hours) in order to obtain the most
>>> accurate result.
>>>
>>> This particular mode of operation is not aimed to be used in
>>> standard methods like VBM. In my project I need to obtain accurate
>>> high resolution "displacement field", which will be used to
>>> transforms particular points from the native space to the MNI space
>>> (for example, the points belonging to a particular tract {xi,yi,zi,
>>> i=1..n} reconstructed by DTI and deterministic tractography
>>> algorithms).
>>> There are any "optimal" configuration files to perform this type of
>>> high resolution registration from the native space to the templates
>>> MNI152_T1_1mm or MNI152_T1_0.5mm?
>>>
>>> Any recommendations would be appreciated,
>>>
>>> Many thanks,
>>>
>>> Erick J. Canales-Rodríguez
>>>
>>> (+34) 93 652 99 99 ext. 255
>>> Unitat de Recerca, Benito Menni CASM
>>> Sant Boi del Llobregat (Barcelona), Spain
>>
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>
> Este mensaje se dirige exclusivamente a su destinatario y puede
> contener información privilegiada o confidencial. Si no es vd. el
> destinatario indicado, queda notificado de que la utilización,
> divulgación y/o copia sin autorización está prohibida en virtud de
> la legislación vigente. Si ha recibido este mensaje por error, le
> rogamos que nos lo comunique inmediatamente por esta misma vía y
> proceda a su destrucción.
>
> Aquest missatge va dirigit exclusivament al seu destinatari i pot
> contenir informació privilegiada o confidencial. Si vosté no és el
> destinatari indicat, li notifiquem que la utilització, divulgació i/
> o còpia sense autorització està prohibida en virtud de la legislació
> vigent. Si ha rebut aquest missatge per error, li preguem que ens ho
> comuniqui el més aviat possible.
>
> Este mensaje se dirige exclusivamente a su destinatario y puede
> contener información privilegiada o confidencial. Si no es vd. el
> destinatario indicado, queda notificado de que la utilización,
> divulgación y/o copia sin autorización está prohibida en virtud de
> la legislación vigente. Si ha recibido este mensaje por error, le
> rogamos que nos lo comunique inmediatamente por esta misma vía y
> proceda a su destrucción.
>
> Aquest missatge va dirigit exclusivament al seu destinatari i pot
> contenir informació privilegiada o confidencial. Si vosté no és el
> destinatari indicat, li notifiquem que la utilització, divulgació i/
> o còpia sense autorització està prohibida en virtud de la legislació
> vigent. Si ha rebut aquest missatge per error, li preguem que ens ho
> comuniqui el més aviat possible.
>
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