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Dear Experts Apologies for cutting in on the discussion. How about using all_FA.nii.gz file that is produced via FSL-TBSS pipeline ? As all_FA.nii.gz is already normalized to MNI space, it seems safe to feed these FA files (after fslsplit) into spm statistics. Thank you in advance for your valuable tips. Kim 2014-02-28 5:16 GMT-08:00 Hasan, Khader M <[log in to unmask]>: > 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 > > > 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.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 > > > 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. >