Save location

[Brady Hunt]

Hi,

I am brand new to plastimatch.  I was able to successfully install on my Windows 10 machine and run the example script for image registration ('plastimatch register command_file.txt').

My command file is as follows:

# b-spline image registration example

[GLOBAL]

fixed=fixed.nrrd

moving=moving.nrrd

img_out=moving_warped.nrrd

xform_out=bspline_coefficients.txt

[STAGE]

xform=bspline

impl=plastimatch

metric=mi

threading=openmp

max_its=30

regularization_lambda=0.005

grid_spac=100 100 100

res=4 4 1

I would like to run this command on a large set of files which are located on an external drive (Y: drive on Windows).  My original data are actually 2D MR cine images which are in DICOM format (approximately 60,000 total files with ~2,000 in each time sequence).

Do you have any tips for running the registration command in batch mode with a large number of input and output files?  Also, is there a recommended way to perform 2D image registration on a cine sequence?

Thanks so much!

- Brady

[Sharp, Gregory C.]

Hi Brady,

 

Second question first.  You don't need to do anything special for 2D images.  They are treated as 3D images, but the vector field will be zero in the third dimension.

 

First question.  Running registration in batch requires a script.  I have added an example to the documentation.  You can find it here:

 

http://plastimatch.org/batch_registration.html

 

Assuming you are registering 2D cine MR vs 2D cine MR, I suggest parameter settings similar to what is in the script.  Indeed, I wrote (a more complex version of) that script for 2D cine MR sequence registration.  I can give a few pointers:

 

- Check the first few frames, some of them may have poor quality and shouldn't be used as a reference frame.

- Use MSE instead of MI, it is a unimodal problem.

- Your cine MR may or may not have actual pixel size / pixel geometry.  Mine didn't, so I set the voxel size to 1, thus grid_spac=4 4 4 gives one control point every 4 pixels.  You may need to adjust this.

 

Good luck,

Greg

 

 

From: plast...@googlegroups.com <plast...@googlegroups.com> On Behalf Of Brady Hunt
Sent: Tuesday, April 20, 2021 4:21 PM
To: Plastimatch <plast...@googlegroups.com>
Subject: [Plastimatch] Save location

 

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[Brady Hunt]

Hi Greg,

Thank you very much! I’ll give it a try and let you know the outcome.

One other naive question. But when I specify file names for my “img_out” and “xform_out”, are those saved in the working directory where plastimatch is called, or somewhere else? I can seem to find those outputs on my disk.

- Brady

On Apr 30, 2021, at 11:30 AM, Sharp, Gregory C. <GCS...@partners.org> wrote:



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[Sharp, Gregory C.]

HI Brady,

Sorry I missed this post.  Yes, they are saved in the current directory.

Greg

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Sent: Friday, April 30, 2021 11:37 AM
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Subject: Re: [Plastimatch] Save location

 

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