Dear SPMers,
 
I'm seraching for a script for creating ROI img under a batch mode (I need just enter the coordinates of the regions). Can someone help me ?
Tao
----- Original Message -----
From: [log in to unmask] href="mailto:[log in to unmask]">Douglas Burman
To: [log in to unmask] href="mailto:[log in to unmask]">[log in to unmask]
Sent: Wednesday, July 09, 2008 6:05 PM
Subject: Re: [SPM] individual functional and anatomical superimposition

Tao,

That's right.  If you additionally want to identify the exact region based upon atlas coordinates, you should run both types of analyses in parallel -- i.e., with and without normalization.


Doug


==============Original message text===============
On Wed, 09 Jul 2008 10:44:47 am CDT "jiang" wrote:

Doug,
Yes, your suggestion helps very much the comprehension of what I have done. thank you!
But another question raised, in this case (without normalisation), does it mean that I cannot use the common atlas coordinates to identify the exact region where are my activations ?
Tao
----- Original Message -----
From: Douglas Burman
To: [log in to unmask]
Sent: Wednesday, July 09, 2008 3:15 PM
Subject: Re: [SPM] noramlisation


Tao,

If you want to superimpose the subject's functional activation on his own anatomical (structural) image, run a set of analyses on images that were realigned and smoothed without normalization. The functional activation can then be superimposed on the structural image.

To avoid loss of resolution for the structural image, it works best to start by coregistering one functional image to the structural (rather than vice versa), then realign all the functional images to this coregistered image. For this analysis, realign and reslice, then smooth the resulting images before running the analysis.

Hope this helps.

Doug

==============Original message text===============
On Wed, 09 Jul 2008 1:51:04 am CDT jiang wrote:

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, s egmentation--coregistre anatomical and mean realigned functional images, use the segmentation parameter to normalise functional and anatomical ones ; 2nd method : nomalise mean functional to EPI t emplet, 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 2 008 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 segmentatio n 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-correcte d 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 correctio n 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"
> > 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 sho ws
> >>
> >> time_units ms
> >> pixdim4 2000.0000000000
> >>
> >> which is correct. After using realign and unwarp, the NIfTI header shows
> >&g t;
> >> 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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