Another option is to get a simple transmission scan in the same run (without repositioning) and to try to register the skull.
Cheers-
Andreas
________________________________________
Von: FSL - FMRIB's Software Library [[log in to unmask]] im Auftrag von Cornelius Werner [[log in to unmask]]
Gesendet: Mittwoch, 16. März 2011 11:11
An: [log in to unmask]
Betreff: Re: [FSL] Normalize DATSCAN to MNI (ideally non-linear)
Dang, the link above only works from within a google search :-(
Find the pic attached (left normal, right parkinson's)
Cheers,
C
On Wed, Mar 16, 2011 at 11:10 AM, Cornelius Werner
<[log in to unmask]> wrote:
> Dear Mark,
>
> that's precisely why I think this will not work - the boundaries are
> NOT equal. In pathological DatScans the volume typically gets smaller
> (particularly the "tail" towards the occiput), while the anatomical
> structure stays the same. See this link for an example:
>
> http://www.medscape.com/viewarticle/735875
>
> or simply google DaTScan in an image search. While I am certainly not
> an PET expert, I seem to remember that DaTScans are somewhat difficult
> to analyze automatically. In our routine, we get semiquantitative
> results by our nuclear medicine staff at best.
>
> Cheers,
> Cornelius
>
> On Wed, Mar 16, 2011 at 10:50 AM, Sven Haller <[log in to unmask]> wrote:
>> Dear Mark
>>
>> Thanks a lot
>> Try this link. I hope that it works
>> http://gallery.me.com/sven.haller/100063
>>
>> Sven
>>
>> On 16 mars 2011, at 10:20, Mark Jenkinson wrote:
>>
>>> 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
>>>>>>
>>>>
>>
>
>
>
> --
> Dr. med. Cornelius J. Werner
> Department of Neurology
> RWTH Aachen University
> Pauwelsstr. 30
> 52074 Aachen
> Germany
>
--
Dr. med. Cornelius J. Werner
Department of Neurology
RWTH Aachen University
Pauwelsstr. 30
52074 Aachen
Germany
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