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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: xuhaibo To: [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 > >> ------------------------------------------------------------------------------ 轻松把Hotmail下载到本地，试试 Windows Live Mail。 立即尝试！