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Chp 41 (Page 41.4) in SPM8 manual has very detailed instruction on how to normalise images to MNI space based on result from new segment tool Tony From: SPM (Statistical Parametric Mapping) [mailto:[log in to unmask]] On Behalf Of Courtney Brown Sent: Thursday, October 28, 2010 8:58 AM To: [log in to unmask] Subject: Re: [SPM] SPM8 Segmentation Issue Thank you for the helpful responses to my post. I have run my images through SPM8 "New Segment," which does indeed improve the quality of the segmented images considerably. I am attempting to continue the pre-processing of these images (specifically, Normalize and Smooth the fMRI images) and am running into a problem: the normalization parameters produced by "New Segment" (seg8.mat) is not recognized as a parameter file for the Normalize and Write step (error code generated pasted below): Running 'Normalise: Write' Failed 'Normalise: Write' Reference to non-existent field 'VG'. In file "/usr/local/share/data/spm/spm8/spm_write_sn.m" (v2534), function "get_xyzmat" at line 430. In file "/usr/local/share/data/spm/spm8/spm_write_sn.m" (v2534), function "spm_write_sn" at line 96. In file "/usr/local/share/data/spm/spm8/config/spm_run_normalise_write.m" (v2312), function "spm_run_normalise_write" at line 25. Running 'Smooth' Done 'Smooth' The following modules did not run: Failed: Normalise: Write My question is: Is there a way to generate a seg_sn.mat file that would be compatible with the Normalize and Write step? Alternatively, is there a more appropriate way to normalize and smooth fMRI images using the parameter file generated from "New Segment?" Thank you in advance, Courtney Brown On Mon, Oct 25, 2010 at 8:17 AM, John Ashburner <[log in to unmask]<mailto:[log in to unmask]>> wrote: Both of these segmentation failures are due to poor initial affine registration. Essentially, if the initial alignment with the tissue probability maps is not so good (maybe because of intensity nonuniformities, large initial misregistrations, or incorrect voxel sizes etc) then the kinds of results we see here may be expected. The algorithm behind the Segment button does not include any knowledge of what would be expected outside the brain, as the tissue probability maps are only of GM, WM and CSF. One of the effects of this is that the initial affine registration may be less robust. If you use SPM8, there is an alternative segmentation routine available from among the toolboxes (with the unimaginative name of "New Segment"). This implementation includes some additional knowledge of non-brain tissues, so is generally more robust. It will eventually become the default segmentation routine, but only after I have written some more code to use the deformation fields it produces for spatial normalisation. Best regards, -John On 23 October 2010 16:10, Courtney Brown <[log in to unmask]<mailto:[log in to unmask]>> wrote: > Hello, > > I am having some difficulty with the segmentation step within SPM8. I am > looking at healthy young adults completing fMRI paradigms. After outputting > grey matter and white matter segmented files from the anatomical image, I > have gotten strange results (please see attached jpeg images). This does not > happen each time I run segmentation, but I have gotten similar output files > on several occasions. I have tried running segmentation with the cropped > anatomical image as opposed to the original anatomical image. The images > above involve the SPM8 segmentation default settings. I have also tried to > adjust some of the segmentation defaults (higher/ lower Bias regularisation, > higher/ lower Bias FWHM), but have gotten similar results in each case. > > My question is: Does anyone have a sense of what would cause these types of > images being outputted after the segmentation step. And furthermore, what > would be the best resolution to this issue in order to adequately preprocess > fMRI images for analysis? > > Any input would be greatly appreciated. > > Thank you, > > Courtney Brown > > Graduate Student > Department of Psychology > University of Georgia ________________________________ IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the intended recipient, please immediately notify us by return email, and delete this message from your computer.