Hi Julie
The default options for segmentation are to use the included SPM
tissue probability maps, which are in MNI/ICBM space. You should be
fine to use icbm_spm2tal.m to convert points.
Jonathan
On Wed, Mar 18, 2009 at 5:32 PM, Julie E McEntee <[log in to unmask]> wrote:
> I did not set a template during normalization. I chose Normalise: Write, using the *seg_sn.mat (from segmentation of the T1) as Parameter File and a*.img files as Images to Write.
>
> I am wondering if it is OK to be using icbm_spm2tal.m to convert the coordinates into Talairach space.
>
> Thanks,
>
> 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: David M White <[log in to unmask]>
> Date: Wednesday, March 18, 2009 9:30 am
> Subject: RE: [SPM] fMRI results in MNI or ICBM space?
> To: Julie E McEntee <[log in to unmask]>
>
>
>> What do you have set as your template image during normalization?
>>
>> David M. White
>> Program Coordinator
>> University of Alabama at Birmingham
>> Psychiatry - Behavioral Neurobiology
>> Neuroimaging and Translational Research Laboratory
>> Sparks Center 501F
>> (205) 996-9813
>> [log in to unmask]
>>
>> -----Original Message-----
>> From: SPM (Statistical Parametric Mapping) [
>> On Behalf Of Julie E McEntee
>> Sent: Wednesday, March 18, 2009 7:59 AM
>> To: [log in to unmask]
>> Subject: [SPM] fMRI results in MNI or ICBM space?
>>
>> Hello List,
>>
>> I am using SPM5 to preprocess/analyze my fMRI images. The following are
>> the preprocessing steps I use:
>>
>> 1) realign (mean only)
>> 2) slice timing (interleaved aquisition, TR = 2, no gap)
>> 3) coregistration estimate T1 and mean functional
>> 4) segmentation of T1
>> 5) write normalize using parameters generated by segmentation
>> 6) smooth using 6 6 6 kernel
>>
>> Are the smoothed images in MNI or ICBM space?
>>
>> Thank-you for yor help,
>>
>> 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
>
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