Certainly! The structural images are already in that zip file I uploaded yesterday (sub03_05_t1 and _t1_brain.nii). The new zip file includes the original EPI (run001.nii.gz), denoised EPI (denoised_data.nii.gz, which is what I used as input for my main 1st-level analysis), fieldmaps (brain-extracted magnitude image, and fieldmap created via fsl_prepare_fieldmaps), and the complete "reg" and "reg_standard" directories from the first-level analysis.
I had trouble putting such a big file onto your server, so I've used dropbox again: https://www.dropbox.com/s/pd1qqiexy2n3qym/regTestPhilip2.zip
Thanks,
Benjamin Philip
On Thu, 30 May 2013 09:55:40 +0000, Mark Jenkinson <[log in to unmask]> wrote:
>Dear Benjamin,
>
>I'm afraid there really isn't enough information in these png files for me to determine the fine details of the registration performance. The brain extraction looks fine though.
>
>Can you please upload the nifti files, including the original fmap, EPI and structural images (as entered into the FEAT GUI) plus the registration output nifti files (e.g. example_func2highres.nii.gz, highres2standard.nii.gz, etc.). Our upload website is:
> https://oxfile.ox.ac.uk/oxfile/work/extBox?id=68312615463381F4C
>
>From this I should be able to work out what can be improved.
>
>All the best,
>Mark
>
>
>On 29 May 2013, at 17:12, Benjamin Philip <[log in to unmask]<mailto:[log in to unmask]>> wrote:
>
>I have some analyses with poor standard-space registration outcomes. "Poor" not "failed"; there are no overt errors on the registration-summary pages, but especially on second-level analysis I see swathes of fMRI-activated voxels outside the brain.
>
>What I've done:
>1) BET, an imperfect but reasonable job (as good as I could get it).
>2) First-level pre-stats separately: including motion-correction, B0 unwarping, and its own pass through registration. I used the output of this for ICA denoising.
>3) I ran first-level stats/post-stats on ICA-denoised data. BBR registration to main structural image, 12dof nonlinear (10mm) to standard space.
>4) I ran a second-level analysis taking a simple average across 4 runs. No clear differences between runs, so I've only included first-level stuff for one run.
>
>What I see:
>1) At the first level stats, a little bit of "leakage" beyond the edge of the brain, but not too bad.
>2) At second level, huge swathes of activation outside the brain.
>
>What I've included in the linked file:
>1) t1 and t1_brain files, illustrating BET
>2) .fsf files for prestats, stats, and second-level analysis
>3) All the PNGs from the registration pages at both levels
>4) Sample stats (thresh_zstat and rendered_thresh_zstat) images from both levels.
>
>Everything appears okay until the second-level stats images, which have huge non-brain activations. Judging by masksum_overlay at the second level, the problem seems to come from registration to standard space... but I'm at a loss how to improve it. Any suggestions or troubleshooting steps would be greatly appreciated!
>
>Files at https://www.dropbox.com/l/KVztbYxsJojB7NQBys3kM9
>
>Thanks,
>
>-----
>Benjamin Philip, Ph.D.
>Postdoctoral Fellow - Freylab
>University of Missouri
>206 Melvin H. Marx Bldg
>1416 Carrie Francke Drive
>Columbia, MO 65211
>[log in to unmask]<mailto:[log in to unmask]>
>
>
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