Yes, thank you for correcting that oversight. And, thank you for sharing the code! That will come in handy.
Warm regards,
Jeff
> On Jul 31, 2018, at 7:20 AM, Auer, Tibor <[log in to unmask]> wrote:
>
> Just one comment:
> The "native-to-MNI transforms generated by the DARTEL" is a two-step approach. The (non-linear) flowfield only transform to the DARTEL study template. You also need to apply the affine template-to-MNI transform to register to MNI space.
>
> Since pipelines like this can be quite complex, you may want to take a look at https://github.com/rhodricusack/automaticanalysis to setup and run neuroimaging (mostly SPM) pipelines efficiently. The https://github.com/rhodricusack/automaticanalysis/blob/master/examples/aa_user_fmri_advanced.m example actually demonstrates normalisation of fMRI data via DARTEL ("piggyback normalization").
>
> 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]
>
>
>
> -----Original Message-----
> From: SPM (Statistical Parametric Mapping) [mailto:[log in to unmask]] On Behalf Of Jeff Browndyke
> Sent: 30 July 2018 15:56
> To: [log in to unmask]
> Subject: Re: [SPM] Dartel/ EPI normalizing
>
> You need to apply the native-to-MNI transforms generated by the DARTEL segmentation/normalization routine to the EPI data. This assumes that you coregistered the T1 to the EPI data for each subject. Doing so will bring your EPI into DARTEL warped MNI space. I like to call the method of structural warping to MNI and then applying the transforms to coregistered data, “piggyback normalization.” This technique works reasonably well when you have degraded or odd EPI images that won’t warp well directly to the SPM EPI template.
>
> Hope this helps,
> Jeff
>
> Jeff Browndyke, Ph.D.
> Duke University Medical Center
>
>
>> On Jul 30, 2018, at 10:44 AM, aral ahmadi <[log in to unmask]> wrote:
>>
>> Dear experts,
>> I have a question regarding normalizing EPIs based on segmented T1s with Dartel . All the segmentation steps and transferring to MNI template been done on T1s with Dartel using spm12, now we are trying to normalize the EPIs images based on what we got from Dartel, but we are not sure how? Any help would be appreciated.
>> Thanks
>> Ara
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