Hello Freesurfers,
I would like to use FreeSurfer to analyse brain morphology in dogs but do not know if the techniques can be applied in this species.
Does anyone have experience using FreeSurfer in dogs, and any tips to get the techniques to work?
Regards, Marjorie Milne
my own experience with analyzing mri scans of dog brains have not been fruitful from the brain morphometry perspective. the reason is that the scan parameters of the brains i worked with were not setup for morphometry (rather, for clinical diagnostics) and so were lacking in major areas, namely the contrast was not setup to discriminate gray matter from white matter (mainly they were T2-like) and the resolution was typically 2.5 to 4.5mm in one plane, which makes it hopeless to reconstruct surfaces or resolve subcortical structures.
but my approach was attempting to use freesurfer tools. it is possible to conduct a morphometry analysis by manually segmenting slices, but this would of course be very time consuming. so if you could get images that are T1-weighted, optimized for gm/wm contrast, and close to 1x1x1mm resolution, then the freesurfer tools could be used. manual work would still be required (akin to work on primate brains).
there are others i know who have tried, so i can put you into contact with them if you want.
n.
On Wed, 2011-07-06 at 09:49 +0000, Marjorie Milne wrote:
Hello Freesurfers,
I would like to use FreeSurfer to analyse brain morphology in dogs but do not know if the techniques can be applied in this species.
Does anyone have experience using FreeSurfer in dogs, and any tips to get the techniques to work?
Regards, Marjorie Milne
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Marjorie,
I don't know of anyone who has used it in dogs, but you could try the monkey stream and see if it works for you (it will disable all the human-specific atlases and such). It will require more manual intervention though
cheers Bruce On Wed, 6 Jul 2011, Marjorie Milne wrote:
Hello Freesurfers,
I would like to use FreeSurfer to analyse brain morphology in dogs but do not know if the techniques can be applied in this species.
Does anyone have experience using FreeSurfer in dogs, and any tips to get the techniques to work?
Regards, Marjorie Milne
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks Nick & Bruce,
Nick - I have high resolution T1W 3D scans, with 1mm voxel size and pretty good grey white matter contrast. Could you put me in touch with those that have used freesurfer on canine brains please?
If I had a canine brain MRI atlas, similar to the Talairach atlas, could I integrate this into Freesufer and use this as my template instead?
Bruce - how do I go about trying the 'monkey stream'?
With thanks, Marjorie.
________________________________________ From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Wednesday, 6 July 2011 11:36 PM To: Marjorie Milne Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FreeSurfer use in dogs
Hi Marjorie,
I don't know of anyone who has used it in dogs, but you could try the monkey stream and see if it works for you (it will disable all the human-specific atlases and such). It will require more manual intervention though
cheers Bruce On Wed, 6 Jul 2011, Marjorie Milne wrote:
Hello Freesurfers,
I would like to use FreeSurfer to analyse brain morphology in dogs but do not know if the techniques can be applied in this species.
Does anyone have experience using FreeSurfer in dogs, and any tips to get the techniques to work?
Regards, Marjorie Milne
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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