adalca / patchregistration Goto Github PK

Hi
I wanted to use this registration for my research. But some libraries mentioned in setup.m file are missing.
Missing libs are :

1. https://github.com/adalca/mgt
2. https://github.com/adalca/mmit
3. https://github.com/adalca/mivt
   Have any idea how to get them?

regards

Hi, Dalca~
Thanks for your wonderful work and codes!
I have a question that how I can get the clinical images and corresponding manual segmentations mentioned in paper?
I hope to hear from you soon~

Hi!
I am trying to use your code to register two histology images. The inputs to the function registerNii are two files named paths.ini and params.ini. I had a look at the parameters in the paths file to change them to refer to my fixed and moving images. However, the paths.ini file seems to be an example input file for registering the images to an atlas. I don't know how I should change this file to perform registration for my pair of images. Would you please guide me in this process? I appreciate that.

Dear Andreea and Adrain,
May I ask you another favor? I am trying to use your algorithm to register renal cancer tissue images using your algorithm. The images are down-sampled to 4098 pixel x 2048 pixel size. I tried different parameter values (patch size, search size, grid spacing, ...) and ran the code. However, I have not achieved the desired registration output yet. I believe I am not using proper values and since the execution take time I thought I shall ask you for advice on the range of values I need to try. May Images look like the image in the following link:
An example of renal cancer tissue images

I have tried the following values:
patch size = 5x5, grid size = 3x3, grid spacing = 3x3, nInnerReps = 3, doAffine = true, method
= resize , nScale = 4, minVolSize = 256, reg = mrf, nStates = complete, metric = sparse, location = 0.001

patch size = 5x5, grid size = 3x3, grid spacing = 3x3, nInnerReps = 3, doAffine = true, method
= resize , nScale = 4, minVolSize = 256, reg = mrf, nStates = 8, metric = sparse, location = 0.01

patch size = 5x5, grid size = 3x3, grid spacing = 3x3, nInnerReps = 3, doAffine = true, method
= resize , nScale = 4, minVolSize = 256, reg = mrf, nStates = 8, metric = seuclidean, location = 0.01

patch size = 7x7, grid size = 3x3, grid spacing = 3x3, nInnerReps = 3, doAffine = true, method
= resize , nScale = 4, minVolSize = 256, reg = mrf, nStates = complete, metric = euclidean, location = 0.001

patch size = 11x11, grid size = 9x9, grid spacing = 7x7, nInnerReps = 3, doAffine = true, method
= resize , nScale = 4, minVolSize = 256, reg = mrf, nStates = complete, metric = sparse, location = 0.01
I appreciate your help and look forward to hearing from you soon.
Best Wishes,
Mahsa