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SPM  July 2008

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Subject:

Re: search for a ROI batch

From:

Guillaume Sescousse <[log in to unmask]>

Reply-To:

Guillaume Sescousse <[log in to unmask]>

Date:

Wed, 9 Jul 2008 19:03:47 +0200

Content-Type:

text/plain

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text/plain (258 lines)

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
>     > >>
>
>
>
>     ------------------------------------------------------------------------------
>     轻松把Hotmail下载到本地,试试 Windows Live Mail。 立即尝试!
>     ===========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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