Projects:DBP2:Harvard:Registration Documentation:Compare - Revision history

Rauscha at 20:44, 28 May 2009

2009-05-28T20:44:00Z

Rauscha: /* Bspline */

2009-05-28T20:40:43Z

Bspline

Rauscha: /* Affine */

2009-05-28T20:38:58Z

Affine

Rauscha: /* Bspline */

2009-05-28T20:36:41Z

Bspline

Rauscha: /* Affine */

2009-05-28T20:15:25Z

Affine

Rauscha: /* Rigid */

2009-05-28T19:49:20Z

Rigid

Rauscha at 19:48, 28 May 2009

2009-05-28T19:48:39Z

Rauscha: /* Bspline */

2009-05-28T15:08:02Z

Bspline

Rauscha at 15:07, 28 May 2009

2009-05-28T15:07:42Z

Rauscha at 19:45, 26 May 2009

2009-05-26T19:45:19Z

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-'''UNDER CONSTRUCTION'''
+This page aims to create a concise comparison of registration methods to show the difference in quality of registration between FSL 4.1 and Slicer 3.3.  All registrations were done with case 01031 T2w as the target and case 01053 T2w as the source image.  We've used only masked images for T2w to DTI baseline because anything else is expected to fail.
 Other types of registrations and a link to the files used can be found [[Projects:DBP2:Harvard:Registration_Documentation|here]].
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 <br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br>
-Bspline registration shows some differences between the two tools.  FSL produces a good registration, only really having trouble in the bottom few slices of the brain when looking at the temporal lobe, and at the very front of the brain, though it does match much of the DTI distortion.  Slicer does not fare as well, working only in the middle portion of the brain.  It does not match the DTI distortion as well, leaving more of the frontal lobe and back of the brain mismatched.  Also, FSL produces a deformation volume that can be used to transform a label map, while Slicer's output transform does not seem to accurately match the volume it created.
+Bspline registration shows some differences between the two tools.  FSL produces a good registration, only really having trouble in the bottom few slices of the brain when looking at the temporal lobe, and at the very front of the brain, though it does match much of the DTI distortion.  Slicer does not fare as well, working only in the middle portion of the brain.  It does not match the DTI distortion as well, leaving more of the frontal lobe and back of the brain mismatched.  Also, FSL produces a deformation volume that can be used to transform a label map, while Slicer's output transform does not seem to accurately match the volume created when directly outputting a volume, meaning label maps cannot be accurately transformed.
 ----

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 ==Bspline==
-[[ File:Case2case target BSPpostAFF FSL Slicer.png |1000px|thumb|left| Rigid-affine-Bspline registration comparison: ##### ]]
+[[ File:Case2case target BSPpostAFF FSL Slicer.png |1000px|thumb|left| Rigid-affine-Bspline registration comparison: Pretty poor for the most part.  Outer boundaries are matched, but little if anything inside is in the same place. Perhaps this is expecte dfor case to case registration. ]]
 <br><br><br><br><br><br><br><br><br><br><br>
 Slicer's masked bspline registration seems ok, though there's maybe a leftward bow to the midsagittal plane, and the back of the brain seems much larger than the target.
 FSL's masked bspline registration seems too large all around, though very well matched on ventricles.

@@ Line 38: / Line 38: @@
 ==Affine==
-[[ File:Case2case target AFFpostRGD FSL Slicer.png |1000px|thumb|left| Rigid-Affine registration comparison: ##### ]]
+[[ File:Case2case target AFFpostRGD FSL Slicer.png |1000px|thumb|left| Rigid-Affine registration comparison: Non-masked are sized by skull and therefore a little off.  Non-masked are done better, mostly well alighed with FSL performing better than slicer. ]]
 <br><br><br><br><br><br><br><br><br><br><br>
-Here there should be some better sizing, as an affine transform will allow more leeway than a rigid.  We shouldn't expect exact matches at this stage however.
+Here we've taken the Rigid images and used them as the source, so that the images you see above have been run through both rigid and affine registration. Here there should be some better sizing, as an affine transform will allow more leeway than a rigid.  Don't expect exact matches at this stage.
 Slicer's masked affine registration is, oddly, more turned than the rigid, with the front tilting definitively left and the top slightly right.  The ventricles match up reasonably well here, however.
 FSL's masked affine registration is for the most part well matched on length, width and orientation.

@@ Line 49: / Line 49: @@
 [[ File:Case2case target BSPpostAFF FSL Slicer.png |1000px|thumb|left| Rigid-affine-Bspline registration comparison: ##### ]]
 <br><br><br><br><br><br><br><br><br><br><br>
-TEXT
+Slicer's masked bspline registration seems ok, though there's maybe a leftward bow to the midsagittal plane, and the back of the brain seems much larger than the target.
 ----

@@ Line 40: / Line 40: @@
 [[ File:Case2case target AFFpostRGD FSL Slicer.png |1000px|thumb|left| Rigid-Affine registration comparison: ##### ]]
 <br><br><br><br><br><br><br><br><br><br><br>
-TEXT
+Here there should be some better sizing, as an affine transform will allow more leeway than a rigid.  We shouldn't expect exact matches at this stage however.
 ==Bspline==

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 =Case to case registration=
 ==Rigid==
-[[ File:Case2case target RGD FSL Slicer.png |1000px|thumb|left| Rigid registration comparison: ###### ]]
+[[ File:Case2case target RGD FSL Slicer.png |1000px|thumb|left| Rigid registration comparison: Mostly good, slight differences in tilt, with masks giving better results than non-masks. ]]
 <br><br><br><br><br><br><br><br><br><br><br>
 All a rigid registration will manage is aligning the two brains in space, it won't account for any anatomic differences.
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 Slicer's masked rigid registration is very close.  There's a slight tip rightward of the top.
 FSL's masked rigid registration seems right on.
 ==Affine==

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 Note: for FSL all files need to be in nifti format.  For me, FSL was interpreting my masked baseline image strangely so I had to flip the nrrd before converting to nifti using unu flip. If you encounter problems while trying this yourself, view your nifti files in FSL before registration to see if they are oriented properly.
 =T2 to Baseline registration=
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 <br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br>
 Bspline registration shows some differences between the two tools.  FSL produces a good registration, only really having trouble in the bottom few slices of the brain when looking at the temporal lobe, and at the very front of the brain, though it does match much of the DTI distortion.  Slicer does not fare as well, working only in the middle portion of the brain.  It does not match the DTI distortion as well, leaving more of the frontal lobe and back of the brain mismatched.  Also, FSL produces a deformation volume that can be used to transform a label map, while Slicer's output transform does not seem to accurately match the volume it created.
 =Case to case registration=