Thanks for this, had been considering that idea, glad to hear it works well.
On 1 May 2015 at 19:37, Simon Jones <[log in to unmask]> wrote:
> If you have many scans I have found it useful to coregister to an average brain first. The MNI brain is larger than normal and has worked less well for me. The attached http://bcni.psychol.cam.ac.uk/~spj24/elderly/ is an average mixed dementia and control group made with DARTEL. This was good for a group of a couple of hundred scans coming from different scanners and voxel sizes though you might want to make your own. When all the brains are coregistered to this you can look at them all as a movie view in spm_ov_browser which works even if the voxel sizes are different. And if one does not work with this as suppose you will have to manually set the origin as others have recommended. The skull stripped may be best.
>
> Simon
>
>> -----Original Message-----
>> From: SPM (Statistical Parametric Mapping) [mailto:[log in to unmask]] On
>> Behalf Of Ian Malone
>> Sent: 29 April 2015 10:49
>> To: [log in to unmask]
>> Subject: Re: [SPM] SPM12 segmentation failures
>>
>> Thanks, I've occasionally used similar tricks in the past, but of course it leads to
>> concerns about reproducibility if you've got a person twiddling things, so I'm
>> hoping there's something that can be done more reliably. I can try an
>> alternative registration strategy to MNI for example.
>>
>> On 28 April 2015 at 16:07, MCLAREN, Donald <[log in to unmask]>
>> wrote:
>> > Ian,
>> >
>> > Use the Display tool to reorient the images to match the origin and
>> > rotation of the MNI template. Then the segmentation should go smoothly.
>> >
>> >
>> >
>>
>> > On Tue, Apr 28, 2015 at 9:35 AM, Ian Malone <[log in to unmask]>
>> wrote:
>> >>
>> >> Hi,
>> >>
>> >> I've been running SPM12 on the accelerated T1 scans from ADNI-2
>> >> (Alzheimer's Disease Neuroimaging Initiative), and found a few (about
>> >> 5 out of 700) images where the segmentation is poor (e.g. attached).
>> >> In most of those cases it looks like there may be a misregistration
>> >> of the underlying tissue prior maps, e.g. extents of csf, wm and gm
>> >> seem shifted in one direction. Loading the mwc classes together with
>> >> the TPM in check reg for this one shows it to be misaligned. Is there
>> >> any advice for dealing with this issue when it arises?
>> >> This being ADNI data there shouldn't be a problem sharing it with
>> >> anyone who wants to take a look.
>> >>
--
imalone
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