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Dear Haibo,
 
Thank you for the extension installation complementary information.
 
About normalisation, I have been instructed by two different methods, one  like written in the manual of SPM, segmentation--coregistre anatomical  and mean realigned functional images, use the segmentation parameter to normalise functional and anatomical ones ; 2nd method : nomalise mean functional to EPI templet, and then use the estimated parameter to normalise the coregiestered anatomical image. Which is better to superimpose the functional image and anatomical one ?
 
Another question how to do to superimpose one's functional image on his own anatomical image ?
 
Thank you for your help
tao
----- Original Message -----
From: [log in to unmask] href="mailto:[log in to unmask]">xuhaibo
To: [log in to unmask] href="mailto:[log in to unmask]">[log in to unmask]
Sent: Wednesday, July 09, 2008 6:01 AM
Subject: Re: [SPM] realign_and_unwarp.m

Dear Julie,
 
The "realign & unwarp " in the preprocessing is independent of brain shape or size, but normalization will be invloved in the brain size or shape due to rescaling. The "realign and unwarp" in pre-processing
has nothing to do with the normalization as mentioned by Karsten. It is better way, as my understanding, to use bias-corrected T1 from segmentation ( or *_seg_sn.mat file) as parameter reference for spatial normalization.
 
Haibo



> Date: Tue, 8 Jul 2008 21:50:59 -0400
> From: [log in to unmask]
> Subject: Re: [SPM] realign_and_unwarp.m
> To: [log in to unmask]
>
> Thank-you for your reply.
>
> The reason I inquired about realign & unwarp is that I am trying to
> determine the optimal spatial preprocessing method for fMRI data acquired
> from 2 groups: healthy controls and patients w/ Huntington's Disease.
> T1-weighted images were also acquired.
>
> My concern is that the patients' brains may be structurally different from
> controls. After realign & unwarp, what would be the best way to estimate the
> warp parameters to use to write normalize the functional images into MNI
> space? If I use the parameters produced by segmentation of the T1 image,
> would the functionals be in MNI space after write normalization? If I use
> normalize: estimate to determine the warp parameters and use the
> bias-corrected T1 from segmentation in addition to an MNI template, would I
> use the mean functional image from realignment as the source image?
>
> I may be making this more complicated than it needs to be. Your advice would
> be greatly appreciated.
>
> Regards,
>
> Julie
>
> -----Original Message-----
> From: Dr. Karsten Mueller [mailto:[log in to unmask]]
> Sent: Tuesday, July 08, 2008 12:06 PM
> To: JULIE E MCENTEE
> Subject: Re: [SPM] pixdim4 in NIfTI header after realign_anbd_unwarp.m
>
> Dear Julie,
>
> thank you for your email. In SPM5, you can decide if you want "realign
> and reslice" or "realign and unwarp". If you decide for unwarp, SPM is
> calculating the EPI distortions from the images. Alternatively, you can
> specify a "voxel displacement map (vdm)" that describes the EPI
> distortions. Thus, you can do the EPI distortion correction while
> applying the realign parameters to the data set.
>
> Those things (realign and unwarp) are the first step in pre-processing
> and have nothing to do with the normalization (into the MNI space). This
> normalization can be done *after* the realignment.
>
> With best wishes to Baltimore,
> Karsten
>
> JULIE E MCENTEE wrote:
> > Dr. Mueller,
> >
> > I am interested in the SPM5 preprocessing option 'unwarp'. Could you
> please tell me why you decided to use it? Did you normalize your images or
> would that be redundant when you use unwarp?
> >
> > Thank-you,
> >
> > Julie
> >
> > Julie E. McEntee, M.A., C.C.R.P.
> > Senior Research Program Coordinator
> > Department of Psychiatry- Neuroimaging
> > Johns Hopkins University School of Medicine
> > 600 N. Wolfe St./ Phipps 300
> > Baltimore, MD 21287
> > Phone: 410-502-0468
> > Fax: 410-614-3676
> >
> > ----- Original Message -----
> > From: "Dr. Karsten Mueller" <[log in to unmask]>
> > Date: Tuesday, July 8, 2008 5:08 am
> > Subject: [SPM] pixdim4 in NIfTI header after realign_anbd_unwarp.m
> > To: [log in to unmask]
> >
> >
> >
> >> Dear Colleagues,
> >>
> >> we are using Realign and Unwarp (spm_realign.m, spm_uw_estimate.m, and
> >> spm_uw_apply.m) with 4D-NIfTI data which gives very nice results.
> >>
> >> However, these m-routines seem to change the NIfTI-header. Before
> >> starting the realignment, our header shows
> >>
> >> time_units ms
> >> pixdim4 2000.0000000000
> >>
> >> which is correct. After using realign and unwarp, the NIfTI header shows
> >>
> >> time_units s
> >> pixdim4 1.0000000000
> >>
> >> This might be a problem when further programs are using the repetition
> >> time from the NIfTI header.
> >>
> >> With best wishes,
> >> Karsten
> >>


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