 |
 |
Since the ICBM_DTI_81 templates are in the ICBM space which is T1w-based, I do not suggest using FA or MD at all. FA contrast is not like T1w where you can see both CSF and gray matter directly.
There are several other methods that have been described (see Hasan et al. 2011 review and References therein)
(A) TBSS -FSL works on "threholded White matter skeleton.
(B) Placing DTI data unto T1w space where segmentations are available FreeSurfer-like (see Walimuni et al. 2011)
(C) Atlas-based methods in native space which provide direct volume estimation (see Hasan et al. 2011 Review; Hasan 2013;2014)
(D) Voxel based anisotropy and diffusivity --the application you need. I use this only for Quality assuarance.
The simplest method in my opinion to accomplish "D" is to use each subject's b0 as target and all other DTI-derived children volumes (i.e. FA, MD, eigenvalues) as objects (these should be scaled appropriately --no negatives)
It works just fine even in SPM2, but we never had success with Dartel results to be frank. Then, may pool all spatially normalized output data and use SPM-like analyses voxel-wise or according to labels in standard space, just make sure you are not mixing voxels due to the excessive and unavoidable
SPM procedures. The ICBM templates as used here just offer landmarks and volumes in the standardized space to check anatomy and assure no mixing of white matter, gray matter and the old good CSF.
This tyope of VBM (which works for both GM and WM and to some extent CSF) is a pseudo-based TBSS which opertates voxel-wise on "white matter voxels skeletonized by thresholding and by connectivity", but does not provide really tracts despite the misleading name.
(E) There are also Tools available in FreeSurfer such as Tracula that can be explored
and (E) of course you can always attempt fiber tarctography in native space along with ROIs (all reviewed and used in the sample applications below).
References
Hasan KM, Walimuni IS, Abid H, Hahn KR. A review of diffusion tensor magnetic resonance imaging computational methods and software tools.
Comput Biol Med. 2011;41(12):1062-72.
Walimuni IS, Hasan KM. Atlas-based investigation of human brain tissue microstructural spatial heterogeneity and interplay between transverse relaxation time and radial diffusivity.
Neuroimage. 2011 Aug 15;57(4):1402-10.
Hasan KM, Ali H, Shad MU. Atlas-based and DTI-guided quantification of human brain cerebral blood flow: feasibility, quality assurance, spatial heterogeneity and age effects.
Magn Reson Imaging. 2013;31(8):1445-52.
Hasan KM, Wilde EA, Miller ER, Kumar Patel V, Staewen TD, Frisby ML, Garza HM, McCarthy JJ, Hunter JV, Levin HS, Robertson CS, Narayana PA.
Serial atlas-based diffusion tensor imaging study of uncomplicated mild traumatic brain injury in adults. J Neurotrauma. 2014;31(5):466-75
Khader M Hasan, PhD
Associate Professor of Radiology
MSE 168, Tel 713 500 7690 (FAX 713 500 7684)
University of Texas Health Science Center at Houston
Medical School
Diagnostic and Interventional Imaging
Magnetic Resonance Imaging Research Division
Diffusion Tensor Imaging Lab, Tel 713 500 7683
http://www.uth.tmc.edu/radiology/faculty/khader-m-hasan/index.html<http://www.uth.tmc.edu/radiology/faculty/hasan.html>
________________________________
From: SPM (Statistical Parametric Mapping) [[log in to unmask]] On Behalf Of Dr Cyril Pernet [[log in to unmask]]
Sent: Friday, February 28, 2014 2:07 AM
To: [log in to unmask]
Subject: Re: [SPM] VBM Normalize step question
http://www.sinapse.ac.uk/<https://urldefense.proofpoint.com/v1/url?u=http://www.sinapse.ac.uk/&k=yYSsEqip9%2FcIjLHUhVwIqA%3D%3D%0A&r=VXYVcWGQQcUORtwYSaJEEMSDYpJQjErvHTp2xHsOge8%3D%0A&m=cXgNnYLbEn%2BuyyoEtknFpiXqH%2FxPE3LExak6HcSeraI%3D%0A&s=31ea21dea8cf7c81f2de899e2483793e749460980f018ab73b6dec71ed0435ed>
Hi Sophuia,
I'm not conviced that VBM on FA maps is really good but .. anyway to answer your question the image to write is any other images which are in the same space as the image to normalize that you want to apply to deformation too --- I would howevrer have a go at DARTEL rather the approach you use (see in the manual there is section on DARTEL)
Cyril
> Dear all,
> I an doing VBM analysis on DTI FA images.
> In the first step, I did normalization on each FA image of controls
> and patients to register them with an FA template (e.g.
> ICBM_DTI_81_FA).
> In the Normalise(Est & Wri) in SPM, I was confused about the
> difference between "Source image" and "Image to write" in a subject
> data. Could I select the same FA image of one subject as the two
> items above?
> In the Estimation options, I chose the ICBM_DTI_81_FA as the template
> image, am I right?
> Looing forward to any help. Thank you!
> Best,
> Sophia
--
Dr Cyril Pernet,
Academic Fellow
Brain Research Imaging Center
Neuroimaging Sciences
University of Edinburgh
Western General Hospital
Division of Clinical Neurosciences
Crewe Road
Edinburgh
EH4 2XU
Scotland, UK
[log in to unmask]
tel: +44(0)1315373661
http://www.sbirc.ed.ac.uk/cyril<https://urldefense.proofpoint.com/v1/url?u=http://www.sbirc.ed.ac.uk/cyril&k=yYSsEqip9%2FcIjLHUhVwIqA%3D%3D%0A&r=VXYVcWGQQcUORtwYSaJEEMSDYpJQjErvHTp2xHsOge8%3D%0A&m=cXgNnYLbEn%2BuyyoEtknFpiXqH%2FxPE3LExak6HcSeraI%3D%0A&s=f1fd94efcb3bdf713d9c063d8abed2c275c040c3cee0f2b4416726a0be10235d>
--
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.