Hi Tao,
you should look at this Marsbar webpage, it should give you ideas:
http://marsbar.sourceforge.net/doc-devel/latest/marsbar/examples/batch/run_tutorial.html.
Regards,
Guillaume
jiang a 閏rit :
> 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:* Douglas Burman <mailto:[log in to unmask]>
> *To:* [log in to unmask] <mailto:[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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> ===========End of original message text===========
>
>
>
>
>
> ===========End of original message text===========
>
>
>
--
___________________________________
Guillaume Sescousse, PhD student
'Reward and decision making' group
Centre de Neuroscience Cognitive
CNRS UMR5229 - UCB Lyon 1
67 Bd Pinel, 69675 Bron, France
tel: 00 33 (0)4 37 91 12 44
fax: 00 33 (0)4 37 91 12 10
http://www.isc.cnrs.fr/dre/
___________________________________
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