Hi
On 1 Sep 2010, at 19:25, Lorena Jimenez-Castro wrote:
> Hello FSL experts,
>
> I would greatly appreciate any hint on the following questions ☺
>
> 1) I did an analysis using Melodic temporal Concatenation, following by randomise using tfce, now for presentation purpose I would like to overlay the xxxxxx_ tfce_corrp_tstat.nii maps on a standard MNI image (MNI152_T1_2mm_brain.nii.gz). How can I do that???
First upsample your stats maps to 1 or 2mm resolution using (e.g.) ApplyXFM
Either in FSLView (and then use screenshots) or with "overlay" followed by "slices".
> in case you need it:
> I did the registration using Flirt and Fnirt, the standard image that I used was MNI152_T1_2mm_brain.nii.gz and I used 4mm for resampling resolution.
> The tfce_corrp_tstat maps have:
> Image Dimensions (X, Y, Z): 45 x 54 x 45
> Voxel Dimensions (X, Y, Z): 4 x 4 x 4
>
>
> 2) I created some ROIs (masks) using the provided structure maps (in atlas tool) in FSLview, because I want to extract only some regions from the xxxxxx_tfce_corrp_tstat maps.
> The question is, how do I need to do the registration to transform that ROI (mask) into the space of my tfce_corrp_tstat maps?. In my case, what are the specific sequence of command that I need to apply in order to do that?
Again - resample either the stats maps or the ROIs so that they have the same dimensions
> 3) If I want to show a rendered map composed by the mask (region affected) overlaid on the MNI152_T1_2mm_brain.nii image. How to show that affected region displaying a red to yellow overlay (red to yellow colors defining increases in the corrected p values)
Easiest in FSLView - see the manual.
Cheers.
>
>
> Thank you so much in advance
>
> Lorena Jimenez, MD.
>
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Stephen M. Smith, Professor of Biomedical Engineering
Associate Director, Oxford University FMRIB Centre
FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
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