I think he wants to transform points with xyz coordinates from diffusion to
MNI space like one could to with img2stdcoord. Which it seems one could do
rapidly now since it appears to support doing many coordinates at once.
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 11:00 AM
To: [log in to unmask]
Subject: Re: [FSL] Advanced normalization options with FNIRT
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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>
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> rogamos que nos lo comunique inmediatamente por esta misma vía y
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>
> 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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