Just to chime in on your specific question of old vs. new segment in
SPM for global values: This is likely to actually make quite a
substantial difference, even for global values. Apart from other
differences in the segmentation routine, the new segment includes more
tissue classes - this is likely to be more accurate, but also can
significantly effect things like TIV (probably because CSF is more
accurately segmented - see supplemental Figure 2 from our NeuroImage
paper).
Best regards,
Jonathan
--
Dr. Jonathan Peelle
Center for Cognitive Neuroscience and
Department of Neurology
University of Pennsylvania
3 West Gates
3400 Spruce Street
Philadelphia, PA 19104
USA
http://jonathanpeelle.net/
On Thu, Jun 28, 2012 at 11:02 AM, Marko Wilke
<[log in to unmask]> wrote:
> ... I would never discourage using any of John's functions ;) but I would
> rather encourage you to explore all available options. As I said, I am
> really impressed by VBM8 when you have good-quality images and don't need
> multispectral processing. I particularly like it for children as it does not
> use priors for segmentation. When it comes to getting global tissue volumes,
> it does not get much more convenient than using VBM8 as it automatically
> writes out text files with the volumes. Disclaimer: have published with
> Christian Gaser ;)
>
>
> Cheers,
> Marko
>
> Michiel de Ruiter wrote:
>>
>> Ok, thanks for this very helpful advice!
>> Would you discourage using the standard segmentation routine altogether
>> (as this doesn't seem to have neck problems)?
>> I just need to calculate GM, WM and CSF volumes, no VBM for the moment.
>> Cheers,
>> Michiel
>>
>> 2012/6/28 Marko Wilke <[log in to unmask]
>> <mailto:[log in to unmask]>>
>>
>>
>> Michiel,
>>
>> another thing you could try is cleaning the maps to only include
>> plausible values. In your screenshot, the upper value is 0.025 and
>> the neck you see seems to be below that, so really low. You could do
>> this in imcalc, doing something like
>>
>> i1 .* (i1 > 0.1)
>>
>> which effectively introduces a lower threshold that is recommended
>> for later statistical analyses anyway. You could also include a step
>> like that in your get_totals script.
>>
>> With regard to Jonathan's remark, you may not usually see this as a
>> function of windowing, but when bringing up new segment's TPM, I am
>> getting 0.0004 for a voxel in the neck, which (to the algorithm in
>> particular) is not 0. You could use an approach such as the above to
>> take care of that, using an even lower value (but take care to
>> modify all volumes in the tpm, and make sure to then potentially
>> increase the values in the background class, and ... in other words
>> and as Jonathan suggested, try not to :)
>>
>> Also, there is a MRF procedure in the "warping & MRF" options in new
>> segment which is usually set to 0 but may help you to remove
>> implausible values such as the ones you see. I have no experience
>> with that, though, as I use vbm8 (which has other options for
>> cleaning etc.).
>>
>> Cheers,
>> Marko
>>
>>
>> Michiel de Ruiter wrote:
>>
>> Dear Jonathan,
>> Thanks a lot for your reply.
>> I did manually reorient the T1 before segmentation.
>> As far as I understand, the tissue probability maps provided by
>> SPM8
>> don't include the neck area so I don't really understand how I
>> should
>> adjust the priors in the neck area.
>> Thanks for the very interesting references as well.
>> Michiel
>>
>> 2012/6/28 Jonathan Peelle <[log in to unmask]
>> <mailto:[log in to unmask]> <mailto:[log in to unmask]
>>
>> <mailto:[log in to unmask]>>>
>>
>>
>> Dear Michiel,
>>
>> > When comparing results for the standard and new segment
>> routines
>> in spm8, I
>> > noticed that with the new segment routine, grey matter is
>> located
>> in the
>> > neck. Admittedly, the probability that a voxel is
>> classified as
>> grey matter
>> > per voxel is very low compared to voxels inside the
>> brain, but it
>> > still influences grey matter volume estimates (e.g., with
>> the
>> get_totals
>> > routine).
>> >
>> > So, should I remove the neck from my T1 scans before
>> using new
>> segment or
>> > does anyone have other tips?
>>
>> We recently (Peelle et al., 2012) used the new segment
>> routine and had
>> some similar issues (though not as bad) with neck gray
>> matter for a
>> few subjects in our initial trials. This was improved by (a)
>> manually
>> repositioning scans to get a good starting estimate and (b)
>> adjusting
>> the priors of gray matter in those regions - they are
>> already very
>> low, but we lowered them even a bit more. This is a bit of a
>> pain and
>> I would recommend not monkeying around with the priors if
>> you can
>> avoid it. However, in our case the combination of the two
>> removed
>> almost all of the neck gray matter artifact.
>>
>> You might also try the new segmentation routine introduced
>> by Rorden
>> et al. (2012), which I believe is a modification of the SPM
>> routine.
>> Although they focus on clinical applications, my impression
>> is that it
>> may reduce some of these artifacts. But I have not yet tried it
>> myself.
>>
>> Finally, if all else fails, then yes, I think trying to
>> remove the
>> neck before segmentation would probably help, but hopefully
>> you can
>> avoid that.
>>
>> References:
>>
>> Peelle JE, Cusack R, Henson RNA (2012) Adjusting for global
>> effects in
>> voxel-based morphometry: Gray matter decline in normal aging.
>> NeuroImage 60:1503-1516.
>>
>> Rorden C, Boniha L, Fridriksson J, Bender B, Karnath H-O (2012)
>> Age-specific CT and MRI templates for spatial normalization.
>> NeuroImage 61:957-965.
>>
>>
>> Hope this helps!
>>
>> Best regards,
>>
>> Jonathan
>>
>> --
>> Dr. Jonathan Peelle
>> Center for Cognitive Neuroscience and
>> Department of Neurology
>> University of Pennsylvania
>> 3 West Gates
>> 3400 Spruce Street
>> Philadelphia, PA 19104
>> USA
>> http://jonathanpeelle.net/
>>
>>
>>
>>
>> --
>> ______________________________________________________
>>
>> PD Dr. med. Marko Wilke
>> Facharzt für Kinder- und Jugendmedizin
>> Leiter, Experimentelle Pädiatrische Neurobildgebung
>> Universitäts-Kinderklinik
>> Abt. III (Neuropädiatrie)
>>
>>
>> Marko Wilke, MD, PhD
>> Pediatrician
>> Head, Experimental Pediatric Neuroimaging
>> University Children's Hospital
>> Dept. III (Pediatric Neurology)
>>
>>
>> Hoppe-Seyler-Str. 1
>> D - 72076 Tübingen, Germany
>> Tel. +49 7071 29-83416 <tel:%2B49%207071%2029-83416>
>> Fax +49 7071 29-5473 <tel:%2B49%207071%2029-5473>
>> [log in to unmask]
>> <mailto:[log in to unmask]>
>>
>> http://www.medizin.uni-__tuebingen.de/kinder/epn/
>> <http://www.medizin.uni-tuebingen.de/kinder/epn/>
>> ______________________________________________________
>>
>>
>>
>
> --
> ____________________________________________________
> PD Dr. med. Marko Wilke
> Facharzt für Kinder- und Jugendmedizin
> Leiter, Experimentelle Pädiatrische Neurobildgebung
> Universitäts-Kinderklinik
> Abt. III (Neuropädiatrie)
>
>
> Marko Wilke, MD, PhD
> Pediatrician
> Head, Experimental Pediatric Neuroimaging
> University Children's Hospital
> Dept. III (Pediatric Neurology)
>
>
> Hoppe-Seyler-Str. 1
> D - 72076 Tübingen, Germany
> Tel. +49 7071 29-83416
> Fax +49 7071 29-5473
> [log in to unmask]
>
> http://www.medizin.uni-tuebingen.de/kinder/epn/
> ____________________________________________________
|
