Dear Donna
Thanks very much for your answer in the previous mail.
now i encounter another problem - Fixed handles appeared again after "Run
Surefit" with "correct errors".
I uploaded my mnc files, chengcc.tar.gz, on
http://pulvinar.wustl.edu/cgi-bin/upload.cgi
MRI file is /chengcc/chengcc1100001.L.full.sMRI.mnc
"/chengcc/SEGMENTATION/chengcc1100001.L.full.segment_corr_corr_corr.patch_corr_corr_corr.mnc"
was produced after correcting
"/chengcc/SEGMENTATION/chengcc1100001.L.full.segment_corr_corr_corr.patch_corr_corr.mnc".
Both's number of handles are 4, although I correct 2 small handles of the
1st one.
Other questions are:
1. Is there any tips to correct handles, especially those looks like huge
"bridge".
2. Is there any way to further crop the image?
Because SureFit doesn't have rotating function while cropping, some
part of the other hemisphere cannot be cropped when image is not straight.
3. I didn't select "fill ventricle", but the lateral ventricle was
segmented as white matter.
any recommendation for fixing it?
4. while drawing volume 2 on volume1, is it possible to adjust the
transparency of volume?
It will be beneficial for us to visually exam the segmentation result.
5. Obtaining surface with precise boundary between white matter and grey
matter is critical for our further study,
taking the file I uploaded for example, any suggestion for it?
Thank you very much
Sincerely,
Po-he
在 Thu, 11 Nov 2004 12:00:02 -0600,
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Today's Topics:
1. about painting error on surface (pohetsn)
2. Re: about painting error on surface (Donna Hanlon)
----------------------------------------------------------------------
Message: 1
Date: Thu, 11 Nov 2004 16:27:56 +0800
From: pohetsn <[EMAIL PROTECTED]>
Subject: [caret-users] about painting error on surface
To: caret-users@brainvis.wustl.edu
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain; format=flowed; charset=big5
Dear all
What I want to do is
1. depressing "Run Surefit"
2. draw segment errors on surface
3. correcting some handle errors
4. saving the new edit
5. depressing "Run SureFit" again (default setting)
6. checking the surface of lately fixed handle errors
7. draw the other segment errors which I havn't fixed
However, at step7, I can't find some file looks like
*.segment.errors.xxxxx.RGB_paint
except the one which generated at step 2.
e.g.
I can find files as follows:
Test.L.occipital.segment_corr2.patch.38499.surface_shape
Test.L.occipital.segment_corr2.patch.38499.topo
Test.L.occipital.segment_corr2.patch.ellipsoid.38499.coord
Test.L.occipital.segment_corr2.patch.ellipsoid.38499.vtk
Test.L.occipital.segment_corr2.patch.fiducial.38499.coord
Test.L.occipital.segment_corr2.patch.fiducial.38499.vtk
Test.L.occipital.segment_corr2.patch.geography.38499.paint
Test.L.occipital.segment_corr2.patch.geography.38499.RGB_paint
Test.L.occipital.segment_corr2.patch.inflated.38499.coord
Test.L.occipital.segment_corr2.patch.inflated-50.38499.vtk
Test.L.occipital.segment_corr2.patch.raw.38499.coord
Test.L.occipital.segment_corr2.patch.raw.38499.vtk
Test.L.occipital.segment_corr2.patch.sulci.38499.RGB_paint
Test.L.occipital.segment_corr2.patch.Surface.38499.spec
but I cannot find anything like
Test.L.occipital.segment_corr2.patch.errors.38499.RGB_paint
in the SURFACE folder.
Anyway, how to do step.7?
It's important while having lots handle errors.
thank you
Sincerely,
phtseng
------------------------------
Message: 2
Date: Thu, 11 Nov 2004 08:08:53 -0600
From: Donna Hanlon <[EMAIL PROTECTED]>
Subject: Re: [caret-users] about painting error on surface
To: "Caret, SureFit, and SuMS software users"
<caret-users@brainvis.wustl.edu>
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain; charset=Big5
Hi Phtseng,
You have drawn attention to a well-known deficit in SureFit: There is no
quick, easy way to update the ERROR_CORRECTION_INTERMEDIATES/*errors*mnc
file, from which the SURFACES/*errors*RGB_paint is generated. This is
the same mnc file that is the default file selection when you press the
Locate Objects button on the Interactive Error Correction tab.
This *errors*mnc file is generated only when you run automatic error
correction, which is the most time-consuming portion of the Run SureFit
routine. When vol2 is loaded (e.g., after you run segmentation and/or
have been patching), then the defaults on the Run SureFit menu change to
skip error correction and prepare to flatten. This is because typically
one doesn't use the Run SureFit menu until you have patched all the
handles and are ready to Prepare to Flatten.
You can change the settings to Correct Errors and Review Surface First,
but this will take a long time to run -- certainly not something you
want to do after fixing each handle. Instead, learn to rely less on the
Locate Objects output and the SURFACES/*errors*RGB_paint coloring on the
surface, and just LOOK for the handles on the inflated surface. Usually,
you can see them if you rotate the surface, zooming and panning as
needed to get a close-up view of all areas. If you can't see the
handles, then they're often not worth fixing.
Is this the SureFit demo volume you are trying to patch? It doesn't have
many handles. What is your handle count? If more than one or two, then
perhaps your patching has introduced some handles. Learning to patch is
certainly the hardest part of learning to use SureFit, and it is
probably harder than flattening, registering, or mapping in Caret. If
you like, I can have a look at your segmentation volume and help you
figure out exactly what to do to fix the handles. If this is not the
demo volume, or if you used cropping parameters (xmin, xmax, ymin, ymax,
zmin, zmax values on the Define VOI tab during Volume Preparation) other
than those specified in the tutorial, then I'll also need your *sMRI.mnc
and *sMRI.params file. Upload these files here:
http://pulvinar.wustl.edu/cgi-bin/upload.cgi
Right now, both John Harwell and I are working on integrating Caret and
SureFit. After SureFit's functions are merged into Caret, then we
envision numerous improvements -- including making patching easier and
more intuitive.
Donna
On 11/11/2004 02:27 AM, pohetsn wrote:
Dear all
What I want to do is
1. depressing "Run Surefit"
2. draw segment errors on surface
3. correcting some handle errors
4. saving the new edit
5. depressing "Run SureFit" again (default setting)
6. checking the surface of lately fixed handle errors
7. draw the other segment errors which I havn't fixed
However, at step7, I can't find some file looks like
*.segment.errors.xxxxx.RGB_paint
except the one which generated at step 2.
e.g.
I can find files as follows:
Test.L.occipital.segment_corr2.patch.38499.surface_shape
Test.L.occipital.segment_corr2.patch.38499.topo
Test.L.occipital.segment_corr2.patch.ellipsoid.38499.coord
Test.L.occipital.segment_corr2.patch.ellipsoid.38499.vtk
Test.L.occipital.segment_corr2.patch.fiducial.38499.coord
Test.L.occipital.segment_corr2.patch.fiducial.38499.vtk
Test.L.occipital.segment_corr2.patch.geography.38499.paint
Test.L.occipital.segment_corr2.patch.geography.38499.RGB_paint
Test.L.occipital.segment_corr2.patch.inflated.38499.coord
Test.L.occipital.segment_corr2.patch.inflated-50.38499.vtk
Test.L.occipital.segment_corr2.patch.raw.38499.coord
Test.L.occipital.segment_corr2.patch.raw.38499.vtk
Test.L.occipital.segment_corr2.patch.sulci.38499.RGB_paint
Test.L.occipital.segment_corr2.patch.Surface.38499.spec
but I cannot find anything like
Test.L.occipital.segment_corr2.patch.errors.38499.RGB_paint
in the SURFACE folder.
Anyway, how to do step.7?
It's important while having lots handle errors.
thank you
Sincerely,
phtseng
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