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Dear Cornelius and Sven, OK, I've seen Sven's images now and have a much better feel for it. The segmentation approach for an individual structural sounds flawed based on Cornelius's observation that the DaTScan does not show all the structure borders clearly. However, the good news is that from the images it is clear that you can find the whole brain in the scan and there main boundaries (at least brain/non-brain) are shown OK. There is clearly a hot-spot in the middle of the scan, but that can be dealt with by (a) hoping that the multi-modal cost functions (mutual information, etc.) will just be OK with this, (b) "inverse" thresholding the image so that intensities over a certain threshold are capped at that value (thus eliminating the bright spots), or (c) using a basal ganglia drived mask (from an individual segmentation or a standard space) to do cost-function weighting and set these areas to zero in the weight (thus ignoring their contribution to the overall alignment). I think that there is a good chance that one of these options would work. All the best, Mark P.S. I wrote this before seeing Cornelius's linked images, which are worse than the one Sven sent wrt brain boundaries. Hopefully most data looks like Sven's images, although it still might be possible to register the images that Cornelius sent. The outer border of the brain is a very good boundary for registration within-subject. On 16 Mar 2011, at 10:10, Cornelius Werner 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 >