I am happy to give a try for the ADNI data if Ian could share it with me.
Vale,
Auer, Tibor M.D. Ph.D.
MRC Cognition and Brain Sciences Unit
15 Chaucer Road
Cambridge
CB2 7EF
United Kingdom
Phone/Work: +44-(0)1223-273613
Mail: [log in to unmask]
-----Original Message-----
From: John Ashburner [mailto:[log in to unmask]]
Sent: Wednesday, April 29, 2015 1:09 PM
To: Tibor Auer; SPM@jiscmail ac. uk
Subject: Re: SPM] SPM] SPM12 segmentation failures
Only if this is actually more robust than the current approach used by the SPM12 segmentation. Would this give less than a 1% failure rate with the same data? This is the proportion of failures that Ian reported.
Best regards,
John
Tibor Auer <[log in to unmask]> wrote:
>How about applying a 6DOF coregistration of the image to the MNI template before segmentation?
>
>Vale,
>
>Auer, Tibor M.D. Ph.D.
>MRC Cognition and Brain Sciences Unit
>15 Chaucer Road
>Cambridge
>CB2 7EF
>United Kingdom
>Phone/Work: +44-(0)1223-273613
>Mail: [log in to unmask]
>
>-----Original Message-----
>From: SPM (Statistical Parametric Mapping) [mailto:[log in to unmask]]
>On Behalf Of John Ashburner
>Sent: Wednesday, April 29, 2015 12:06 PM
>To: [log in to unmask]
>Subject: Re: [SPM] SPM] SPM12 segmentation failures
>
>Usually, the AC is not particularly close to the centre of the magnetic field. I guess I could shift the default starting estimates so that they better reflect how subjects are typically positioned in the scanner. This might be a bit messy though, and would require a bit of user re-education.
>
>Alternatively, I could have used a two-pass procedure that re-ran the affine registration for all subjects, using starting estimates based on a mean or median of the first pass solutions. Many would not like this approach because they want the same answer irrespective of which scans were processed together.
>
>There's always a trade-off about how general to make things. For example, I could make the affine registration more robust for T1w data, at the expense of it failing badly when applied to other image contrasts. Simple things, such as automatically moving the centre of mass of the images would work for some data, but not others. If an algorithm has to handle both T1 maps as well as R1 maps (where T1 = 1/R1), then assumptions about background signal being close to zero can not be made.
>
>Bottom line: fix the headers and things will work better. This fix does not need to be especially accurate, so I doubt that the twiddling of different users will result in systematically different segmentations.
>
>Best regards,
>John
>
>
>Ian Malone <[log in to unmask]> wrote:
>>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
>>http://ibmalone.blogspot.co.uk
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