Hi Arjan,
Thank you much for your response. i looked at torsion but I haven't yet figured
how meaningfully compare them between 2 different centerlines. Another aspect I
discussed with a friend and he suggested I look at the angle between the two
vectors. So if I have 2 comparable points on the 2 different centerlines, I
could look at the angle between the two vectors (FrenetTangent) at those 2
points. I think the angle should be meaningful as long as the centerlines are
registered.
Thanks again for your support,
Manasi
________________________________
From: Arjan Geers [ajge...@gmail.com]
Sent: Sunday, June 10, 2012 8:44 AM
To: Ramachandran, Manasi
Cc: Luca Antiga; vmtk-users@lists.sourceforge.net
Subject: Re: [vmtk-users] Problem with VMTKcenterlinegeometry
Hi Manasi,
Differential geometry isn't my field, but perhaps have a look at the torsion
data provided by vmtkcenterlinegeometry. Torsion is the rate of change of the
curve's osculating plane. Apart from orientation and position, the curvature
and torsion uniquely define a curve in space (fundamental theorem of space
curves).
Hope this points you in the right direction,
Arjan
On Sun, Jun 10, 2012 at 6:06 AM, Ramachandran, Manasi
<manasi-ramachand...@uiowa.edu<mailto:manasi-ramachand...@uiowa.edu>> wrote:
Hi Arjan,
Thanks for the response. Plotting curvature vs abscissa seems to be very useful
and I can pick a few points to visualize on Slicer as well.
I have another silly-tensor-algebra question. Perhaps you will have an answer
for me. My aim is to get change in curvature between the two centerlines but I
want to incorporate rigid body motion between them if any (for eg. twisting of
vessels after stenting that wasn't present before). To elaborate the example,
if I have the same curvature at two comparable points on the two centerlines,
but the directions have completely changed, I want to account for this in my
calculation. Is there a way for me to incorporate change in direction (of a
comparable point between 2 centerlines) into the curvature mangnitude?
Thanks again for your support,
Manasi
________________________________
From: Arjan Geers [ajge...@gmail.com<mailto:ajge...@gmail.com>]
Sent: Friday, June 08, 2012 11:53 AM
To: Ramachandran, Manasi
Cc: Luca Antiga;
vmtk-users@lists.sourceforge.net<mailto:vmtk-users@lists.sourceforge.net>
Subject: Re: [vmtk-users] Problem with VMTKcenterlinegeometry
Hi Manasi,
That's an interesting problem.
Find attached a screenshot of Paraview. To manually select a point, you can
either search in Spreadsheet View (upper right panel) or use the point selector
(red circle).
Spreadsheet View shows the pointdata of the selected point. One of the data
arrays is 'Curvature'. Another one is named 'FrenetTangent', which contains the
vector you're looking for.
NB: I suspect it might be a bit tricky to compare centerlines from two
different images. To find a correspondence between the two centerlines, you
could perhaps use a bifurcation as reference point. Use
vmtkcenterlineoffsetattributes to offset the 0 abscissa to the bifurcation
origin. You can then plot the curvature of both centerlines as function of the
abscissa. The lower right panel in the screenshot shows an example of such a
plot for one centerline.
Good luck with it,
Arjan
On Tue, Jun 5, 2012 at 10:23 PM, Ramachandran, Manasi
<manasi-ramachand...@uiowa.edu<mailto:manasi-ramachand...@uiowa.edu>> wrote:
Hi Luca and Arjan,
Thank you for your responses. I tried a couple of things you suggested and I am
still confused. Perhaps, I should explain my problem a little better.
I have 2 centerlines that I want to compare. These centerlines were obtained
from 2 differents CTs of vessels with a stent and without a stent (same vessel
imaged twice - once with stent and once without stent). I want to compare how
curvatures varies between these 2. Is there a way to pick points along each
centerline manually and look at the curvatures at those specific points? Also,
I want to capture directionality of vessel to see if the vessel has twisted
after stent deployment. So in addition to the curvature scalar, which vector
should I be looking at for the orientation of the centerline at that picked
point?
I hope I am explaining my question a little better. Please let me know what you
think.
Thank you for help,
Manasi
________________________________
From: Luca Antiga [luca.ant...@orobix.com<mailto:luca.ant...@orobix.com>]
Sent: Friday, May 04, 2012 6:53 AM
To: Arjan Geers
Cc: Ramachandran, Manasi;
vmtk-users@lists.sourceforge.net<mailto:vmtk-users@lists.sourceforge.net>
Subject: Re: [vmtk-users] Problem with VMTKcenterlinegeometry
Hi all,
Arjan is right, if the common tract is the same, working with abscissas is the
most robust solution. Unfortunately
I don't think there is a solution out of the box for what you want to do,
although there are several scripts and
classes that use the abscissa to split, measure and do all sorts of operations.
For instance, vmtkpointsplitextractor will split centerlines based on the
proximity to a physical point in space, which
is not what you need but it uses the same ingredients.
So, instead of Paraview you could also use Python directly, it depends on how
appealing this possibility looks to you
and whether this is a one-shot need for you or not.
To add a bit of answer to Arjan's answer on output formats, you could use
vmtksurfacewriter -ofile foo.dat -celldata 1
which, instead of one line per point containing coordinates and point data
arrays, will print one line per cell containing
the cellId and cell data arrays (including curvature, torsion and tortuosity).
Hope this helps
Luca
On May 3, 2012, at 4:18 PM, Arjan Geers wrote:
Hi Manasi,
To answer your second question:
Let's assume a vessel with a single bifurcation. Before the bifurcation, the
two centerlines will indeed follow approximately the same path. In other words,
nearby points on CL1 and CL2 should have approximately the same abscissa.
'Approximately', because the exact path depends on the sampling of the
centerline.
To answer your first question:
Let's assume the sampling of the two centerlines is exactly the same (it seems
that the standard output of vmtkcenterlines is such). Sort the points by
abscissa in ascending order (for example in Paraview's Spreadsheet View).
You'll see that at first the points on row 2n and 2n+1 are the same (n =
0,1,2,...). Once CL1 and CL2 start to deviate, the points will be different.
But... this approach is pretty ugly. Not knowing your goal I can't be sure, but
I actually doubt the point you'll find is very meaningful (correct me if I'm
wrong :-) ). It's not unlikely that there is a more appropriate solution
readily available in VMTK. To familiarize yourself with the possibilities, I
would recommend you to go through the tutorials "Computing Centerlines",
"Branch Splitting", and "Geometric Analysis".
Hope this helps,
Arjan
On Wed, May 2, 2012 at 11:55 PM, Ramachandran, Manasi
<manasi-ramachand...@uiowa.edu<mailto:manasi-ramachand...@uiowa.edu>> wrote:
Hi Arjan,
Thank you so much for your reply. I liked the idea of using centerline
attributes to use L and D.
Along the same lines, I was hoping I could also discuss the possiblility of
locating the same point on 2 different centerlines. For example, say I have CL1
which is a straight line and say CL2 which turns to 90 deg at some point. I
want to locate the point where the CL2 turns and find the same point on CL1.
Can I do this using D and L also?
To elaborate a little more, let us assume that both centerlines start at the
same point (x,y,z). Then, if I calculate L at one point (x2,y2,z2) in CL2 and
then find the same L and pick the corresponding point (x1,y1,z1) on CL1, will
(x1,y1,z1) and (x2,y2,z2) be approximately the same in physical space?
Thank you again for your time and support,
Manasi
________________________________
From: Arjan Geers [ajge...@gmail.com<mailto:ajge...@gmail.com>]
Sent: Thursday, April 26, 2012 5:46 PM
To: Ramachandran, Manasi
Cc: vmtk-users@lists.sourceforge.net<mailto:vmtk-users@lists.sourceforge.net>
Subject: Re: [vmtk-users] Problem with VMTKcenterlinegeometry
Hi Manasi,
If you save the output as *.vtp and open it in Paraview, you'll see that both
tortuosity and length are cell data. They only have one value per cell, i.e.
centerline. All other variables are point data, defined at each point of the
centerline.
>From the looks of it, cell data is not written to *.tec or *.dat. If your goal
>is to obtain either the length or tortuosity of a centerline, I'd recommend
>using *.vtp.
Alternatively, you could run vmtkcenterlineattributes and obtain the length in
Tecplot by picking the abscissa value at the outlet (L), assuming the abscissa
at the inlet is 0. From the start/end coordinates of the centerline you could
calculate the Euclidean distance between the in- and outlet (D). The tortuosity
(Chi) would then be Chi = L/D - 1 (Piccinelli TMI 2009).
Hope this helps,
Arjan
On Thu, Apr 26, 2012 at 11:46 PM, Ramachandran, Manasi
<manasi-ramachand...@uiowa.edu<mailto:manasi-ramachand...@uiowa.edu>> wrote:
Hi Arjan,
Thank you for the reply. I ran this command:
vmtkcenterlinegeometry -ifile
C:/Users/manasi.ramachandran/Documents/30677/stented/Negative20/stented_Series5_Negative20_levelsets_cl_CL.vtp
-smoothing 1 -iterations 10 -outputsmoothed 1 -ofile
C:/Users/manasi.ramachandran/Documents/30677/stented/Negative20/stented_Series5_Negative20_levelsets_cl_CLGM.tec
I can now get data printed on the tec file. There is no length or Tortuosity
information though. Here are first few lines of my tec file:
VARIABLES =
X,Y,Z,MaximumInscribedSphereRadius,EdgeArray0,EdgeArray1,EdgePCoordArray,Curvature,Torsion,FrenetTangent0,FrenetTangent1,FrenetTangent2,FrenetNormal0,FrenetNormal1,FrenetNormal2,FrenetBinormal0,FrenetBinormal1,FrenetBinormal2
ZONE N=805,E=0,F=FEPOINT,ET=TRIANGLE
375.212860107 127.314727783 -840.130249023 4.43752339446 5774.0 5774.0 0.0 0.0
0.0 -0.794417157975 0.0212929549817 -0.606999167366 0.581361416428
0.315991613505 -0.749778769827 0.1758416407 -0.948523015147 -0.263408062013
375.533172607 127.303581238 -839.876281738 4.56642718039 1163.0 1163.0 0.0
0.106633669157 0.0 -0.794417157975 0.0212929549817 -0.606999167366
0.581361416428 0.315991613505 -0.749778769827 0.1758416407 -0.948523015147
-0.263408062013
What am I doing wrong? Why am I not getting Length and Tortuosity to print
into the file.
Thank you for your help,
Manasi
________________________________
From: Arjan Geers [ajge...@gmail.com<mailto:ajge...@gmail.com>]
Sent: Thursday, April 26, 2012 11:44 AM
To: Ramachandran, Manasi
Cc: vmtk-users@lists.sourceforge.net<mailto:vmtk-users@lists.sourceforge.net>
Subject: Re: [vmtk-users] Problem with VMTKcenterlinegeometry
Hi Manasi,
The not-so-elegant solution to your problem may be here:
http://sourceforge.net/mailarchive/message.php?msg_id=28032510
Open the file .\vmtk 0.9.0\lib\vmtk\vmtk\vmtkcenterlinegeometry.py in a text
editor and add the following lines near the end of the file:
centerlineGeometry.SetLengthArrayName('Length')
centerlineGeometry.SetTortuosityArrayName('Tortuosity')
Run the following in PypePad to get the desired output:
vmtkcenterlinegeometry -ifile cl.vtp -smoothing 1 -iterations 10
-outputsmoothed 1 -ofile clgm.tec
Notice that you should leave out of your script "-lengtharray Length" and
"-tortuosityarray Tortuosity",because those array names are now hard-coded.
Otherwise, you will receive again the error message: "vmtkcenterlinegeometry
error: unknown option -lengtharray"
Optionally, you could leave out "-curvaturearray Curvature", because the
default value is 'Curvature'. And you could leave out "-i Centerlines", because
you already specify the centerline with "-ifile cl.vtp".
Hope this helps,
Arjan
On Thu, Apr 26, 2012 at 3:04 PM, Ramachandran, Manasi
<manasi-ramachand...@uiowa.edu<mailto:manasi-ramachand...@uiowa.edu>> wrote:
Hi,
I am using VMTK0.9 on windows 7 (64 bit). I have some problem using
vmtkcenterlinegeometry.
I ran this command:
vmtkcenterlinegeometry -i Centerlines -ifile
stented_Series5_Negative20_levelsets_cl_CL.vtp -lengtharray Length
-curvaturearray Curvature -tortuosityarray Tortuosity -smoothing 1 -iterations
10 -outputsmoothed 1 -ofile stented_Series5_Negative20_levelsets_cl_CLGM.tec
And it will not detect most parameters. Here is the message I get:
Creating vmtkCenterlineGeometry instance.
Automatic piping vmtkcenterlinegeometry
Parsing options vmtkcenterlinegeometry
vmtkcenterlinegeometry error: unknown option -lengtharray
vmtkcenterlinegeometry : compute the local geometry of centerlines in
terms of curvature and torsion
Input arguments:
-id Id (str,1); default=0: script id
-handle Self (self,1): handle to self
-disabled Disabled (bool,1); default=0: disable execution and
piping
-i Centerlines (vtkPolyData,1): the input centerlines
-ifile CenterlinesInputFileName (str,1): filename for the default
Centerlines reader
-curvaturearray CurvatureArrayName (str,1); default=Curvature: name
of the array where curvature values have to be stored
-torsionarray TorsionArrayName (str,1); default=Torsion: name of
the array where torsion values have to be stored
-frenettangentarray FrenetTangentArrayName (str,1);
default=FrenetTangent: name of the array where tangent vectors of
the Frenet reference system have to be stored
-frenetnormalarray FrenetNormalArrayName (str,1);
default=FrenetNormal: name of the array where normal vectors of
the Frenet reference system have to be stored
-frenetbinormalarray FrenetBinormalArrayName (str,1);
default=FrenetBinormal: name of the array where binormal vectors
of the Frenet reference system have to be stored
-smoothing LineSmoothing (bool,1); default=0
-outputsmoothed OutputSmoothedLines (bool,1); default=0
-iterations NumberOfSmoothingIterations (int,1) >= 0; default=100
-factor SmoothingFactor (float,1) >= 0.0; default=0.1
-ofile CenterlinesOutputFileName (str,1): filename for the default
Centerlines writer
Output arguments:
-id Id (str,1); default=0: script id
-handle Self (self,1): handle to self
-o Centerlines (vtkPolyData,1): the output centerlines
-curvaturearray CurvatureArrayName (str,1); default=Curvature: name
of the array where curvature values are stored
-torsionarray TorsionArrayName (str,1); default=Torsion: name of
the array where torsion values are stored.
And when I try running the basic command with only -ifile and -ofile, I get an
empty .tec file. I dont know if it has anything to do with running VMTK on
windows. I am able to run vmtkcenterlineattributes successfully. Please let me
know if anyone else has had the same problem and how you tried to fix it.
Thanks,
Manasi
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