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FSL  March 2011

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Subject:

Re: Normalize DATSCAN to MNI (ideally non-linear)

From:

Mark Jenkinson <[log in to unmask]>

Reply-To:

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

Date:

Wed, 16 Mar 2011 09:20:07 +0000

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (91 lines)

Dear Sven,

It will all be about whether you can see details in the images of
anatomical boundaries like in the MRI or not.  Certainly the more
"different" the images are and the less details you have in them
the more it will be absolutely essential to register them to another
within-subject image (using 6 dof or similar) as non-linear registration
requires highly detailed images that show the same structures in
each.

One approach might be (but I can't say for sure without seeing the
images) to segment the basal ganglia in the T1-weighted image and
use this as a registration target.  However, this would only be appropriate
if the DATSCAN clearly showed only these boundaries and had them
close to the anatomical boundaries.

As for showing an image - can you post it somewhere on the web and 
put the link to it in the email.  It is not possible to attach anything but the 
smallest attachments to the list (to avoid everyone's inbox getting swamped).

All the best,
	Mark


On 16 Mar 2011, at 09:10, Sven Haller wrote:

> Dear Mark
> 
> Thank you very much for your e-mail
> 
> In fact the DaTScans are very different to "normal" SPECT or PET, e.g. FDG PET. In the latter you have activity in the entire brain, so I think that normalization to a T1 (maybe after BET) should be possible (although I have no personal experience here).
> 
> The image of a DaTScan is fundamentally different (see attachment). In fact activity is present only in the basal ganglia. I think that therefore the procedure to normalize the scans should be very different.
> 
> I like FSL, and I would like to analyze VBM and TBSS. Therefore it would be best to analyze the DaTScan also in FSL, followed by a RANDOMISE analysis
> 
> Any help is highly appreciated
> 
> Sven
> 
> PS: The image was refused (too large). Maybe I can send it to you in another way??
> 
> 
> On 16 mars 2011, at 09:29, Mark Jenkinson wrote:
> 
>> Dear Sven,
>> 
>> I have no direct experience of DATSCANs but I assume they are similar
>> to general SPECT or PET scans.  We have had success registering
>> SPECT/PET to MRI before.  It is always better to register the SPECT/PET
>> to that subject's MRI using 6 DOF with FLIRT and a cost function like
>> mutualinfo or normmi.  I would normally choose the best T1-weighted
>> scan as the reference, but it may depend on what features are most
>> clearly seen in your DATSCAN.
>> 
>> Once you've got a good registration of your DATSCAN to your MRI, 
>> then you can register the MRI to the MNI standard space image.
>> This registration can be done with non-linear (FLIRT then FNIRT)
>> whereas it is usually very, very bad to try and register the SPECT/PET
>> with non-linear directly as there are very few features there to drive
>> that registration.
>> 
>> When you have the two registrations then you can combine them with
>> convertwarp to get a non-linear registration from the DATSCAN to
>> the MNI standard space.
>> 
>> I do not know what you want in terms of a "specific template of the
>> basal ganglia" but we have several atlases in FSL, and they include
>> basal ganglia parcellations.
>> 
>> All the best,
>> 	Mark
>> 
>> 
>> 
>> On 16 Mar 2011, at 07:37, Sven Haller wrote:
>> 
>>> Dear all
>>> 
>>> I would like to normalize DATSCANs to MNI standard space
>>> I also have 3DT1 (easy using FSLVBM) and DTI (easy using TBSS).
>>> 
>>> Are there any existing tools for FSL for DATSCANs?
>>> Is there a specific template of the basal ganglia?
>>> Any experience whether it is better to perform a linear registration DATSCAN to DTI, and then use the non-linear registration of TBSS, or better directly register DATSCAN to NMI? In that case, how? Linear or non-linear?
>>> 
>>> Any help is highly appreciated
>>> 
>>> Sven
>>> 
> 

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