Dear Jay,
Have a look at spm_mesh_transform.m (a basic wrapper above spm_swarp.m);
the coordinates will have to be stored in a 'vertices' field of a struct.
Best regards,
Guillaume.
On 31/07/18 20:26, Dubb, Jay wrote:
>
> Hi Tibor,
>
>
> Thanks for the links and tips. Now that I've read up on these topics and
> played around a bit more with SPM, I have a more specific question:
>
>
> I ran Normalization in SPM12 for my structural volume named rT1.nii and
> got as output the files y_rT1.nii and wrT1.nii. I checked the
> registration of the normalized subject volume (wrT1.nii) against the
> MNI152 template using the SPM Check Reg and see that it looks accurate.
>
>
> My question is, do you know how I would apply the output of
> normalization in a Matlab script to the coordinates of the initial
> subject volume rT1.nii, to calculate the corresponding MNI coordinates.
>
>
> Thanks again,
>
> Jay
>
>
>
>
>
>
> ------------------------------------------------------------------------
> *From:* SPM (Statistical Parametric Mapping) <[log in to unmask]> on
> behalf of Auer, Tibor <[log in to unmask]>
> *Sent:* Tuesday, July 31, 2018 7:14 AM
> *To:* [log in to unmask]
> *Subject:* Re: [SPM] Advice for SPM beginner on how to normalize
> structural volumes
>
>
> Hi Jay,
>
>
>
> Ad a.: I recommend you to read the corresponding section of the SPM
> manual and/or the SPM book
> (https://www.fil.ion.ucl.ac.uk/spm/doc/books/hbf2/). There also other
> useful online materials. Se e.g. mine:
> http://www.cubic.rhul.ac.uk/wiki/lib/exe/fetch.php?media=fmri:5_pre-processing.pdf(slide
> 9 and onwards).
>
>
>
> Ad b.: You can try mailing list archive. E.g. for DARTEL (you mentioned
> non-linear transformations):
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=spm;2d6e16b4.1202
>
>
>
> Vale,
>
> Tibor
>
>
>
> *Auer, Tibor M.D. Ph.D.*
>
> *Research Fellow in MRI*
>
> *Department of Psychology*
>
> Royal Holloway University of London
>
> Egham Hill
>
> Egham
>
> TW20 0EX
>
> United Kingdom
>
> +44-1784-27-*6594*
>
> [log in to unmask] <mailto:[log in to unmask]>
>
>
>
>
>
> *From:*SPM (Statistical Parametric Mapping) [mailto:[log in to unmask]]
> *On Behalf Of *Dubb, Jay
> *Sent:* 30 July 2018 23:39
> *To:* [log in to unmask]
> *Subject:* [SPM] Advice for SPM beginner on how to normalize structural
> volumes
>
>
>
>
>
> Hello dear SPM users,
>
>
>
> I am new to SPM. I am looking for advice about some relatively simple
> examples of how one could use the SPM12 batch script to convert
> structural volume native coordinates, say T1.nii, to MNI space. My
> MATLAB graphical application displays individual subjects' head
> and brain in 3D in their native space. It allows users to hide the head
> and click on any location on the brain. I want to add the ability to
> display the MNI152 coordinates which correspond to the selected
> native cortical locations. (Even though it's a MATLAB application, it
> has some parts which tie it to Windows, therefore I am not looking at
> applications such as FSL and FNIRT, which are Linux-based.)
>
>
>
> I was told that I have to do segmentation and then normalization. Maybe
> coregistration as well, although unclear about that too. Or can I do
> ONLY the normalization step with T1.nii as input?
>
>
>
> My questions are:
>
>
>
> a) What steps are needed to do the MNI normalization for my purposes (I
> only care about single subject structural NIFTI volumes, No fMRI)
>
>
>
> b) How would one use the output of the normalization workflow in a batch
> script to do the coordinate transformation to MNI? Since normalization
> involves warping, and non-linear transformations, it's not as simple as
> applying an affine 4x4 transformation matrix to my native coordinates
> ... as far as I understand.
>
>
>
> Any advice would be greatly appreciated...
>
>
>
> Jay
>
>
>
>
>
--
Guillaume Flandin, PhD
Wellcome Centre for Human Neuroimaging
University College London
12 Queen Square
London WC1N 3BG
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