similar to: New package for medical image manipulation: tractor.base

Dear all, There have been some recent major updates to the TractoR and RNiftyReg packages, which are available for medical image analysis applications. If you use R for these purposes, I hope you will find the updates useful. RNiftyReg is an image registration package, which provides a clean R-like interface to the NiftyReg library developed at University College London [1]. It is aimed at

Dear all, There have been some recent major updates to the TractoR and RNiftyReg packages, which are available for medical image analysis applications. If you use R for these purposes, I hope you will find the updates useful. RNiftyReg is an image registration package, which provides a clean R-like interface to the NiftyReg library developed at University College London [1]. It is aimed at

Dear all, The version of readBin() in R-devel includes a use of match(), through `%in%`, which can affect its performance significantly. By using primitives instead of the rather expensive call to match(), I reduce the time spent inside readBin() by more than 30% in some of my code (part of the tractor.base package). A simple patch that does this is given below. This passes "make

Dear all, For an open-source project that I'm working on (1), which uses R for all its heavy lifting but includes a wrapper shell script, I was hoping to find a way to capture all warnings (and, in fact, errors too), and handle them in my own way. I realise I can do this for a single expression using something like: > f <- function(w) print(w$message) >

Dear all, I have asked before, in R-help [1], about a way to create an interactive session in which commands are taken from a file or standard input - like R CMD BATCH but additionally allowing user input - but there was no response to that question, and the workarounds that I have found (using "expect", creating a temporary .Rprofile) are ugly and problematic. With the

Dear all, I am trying to create an environment object with additional attributes, viz. Foo <- structure(new.env(), name="Foo") Doing this in a standard session works fine: I get the environment with attr(,"name") set as expected. But if the same code appears inside a package source file, I get just the plain environment with no attributes set. Using a non-environment

Dear John and others, I've been wondering about whether there's any way to indicate a "nil" reference class object, which will represent "no value", and be tested for, but not fail the internal type checking. NULL is the obvious choice (or seems so to me), but can only be used if an explicit class union is created: > Foo <- setRefClass("Foo") > Bar

dcemri 0.10 has been released on CRAN "dcemri" is (to the best of my knowledge) the first public-domain software package for the quantitative analysis of dynamic contrast-enhanced MRI (DCE-MRI) and diffusion-weighted MRI (DW-MRI or DWI). Data import and export is availble for ANALYZE or NIfTI data formats (sorry, no DICOM). Images are stored in neurological format regardless of the

dcemri 0.10 has been released on CRAN "dcemri" is (to the best of my knowledge) the first public-domain software package for the quantitative analysis of dynamic contrast-enhanced MRI (DCE-MRI) and diffusion-weighted MRI (DW-MRI or DWI). Data import and export is availble for ANALYZE or NIfTI data formats (sorry, no DICOM). Images are stored in neurological format regardless of the

The first release of oro.dicom (v0.2.4) is now available for download from CRAN. This is a major revision and improvement that replaces the previous DICOM package. New features include: * Increased speed * Uploading only header information (for restricted memory situations) * Reading implicit value representations (VR's) * Parsing SequenceItem tags (undefined lengths are allowed) *

The first release of oro.dicom (v0.2.4) is now available for download from CRAN. This is a major revision and improvement that replaces the previous DICOM package. New features include: * Increased speed * Uploading only header information (for restricted memory situations) * Reading implicit value representations (VR's) * Parsing SequenceItem tags (undefined lengths are allowed) *

Dear all, In R-devel (2011-09-23 r57050), I'm running into a serious problem with seek()ing on connections opened with gzfile(). A warning is generated and the file position does not seek to the requested location. It doesn't seem to occur all the time - I tried to create a small example file to illustrate it, but the problem didn't occur. However, it can be seen with a file I use for

Hello there! I hope there is someone out there who is using the DICOM package. When Im trying to read my a DICOM file (MRI-data) I always get this error: > dicom.info("~/myfile") Error in readBin(fid, integer(), length, size = 1) : invalid value of 'n' The DICOM files that come with the DICOM package work just fine. I already tried both endian options. I can view my

Dear all, Is there a way to force R CMD INSTALL to ignore ~/.Rprofile and similar? I presume it sources these startup files for a reason, but I've found that it can cause confusion or problems. In particular, my ~/.Rprofile loads a few packages which I very frequently use, but this stops me from installing new versions of their dependencies; viz. $ R CMD INSTALL tractor.base * installing to

Hello, I have the following problem. After a PACS upgrade in our hospital, the dynamic 3D images acquired after contrast media injection with a 3T Philips MRI are all saved in a single 4D file instead of a series of 2D images containing multiple 3D images over time. I used to convert this series of 2D dicom images in the format nfti with oro.dicom. However, I am no longer able to make oro.dicom

Dear all, I have a simple front-end program which uses the APIs described in section 8 of "Writing R Extensions" to deviate from the standard R behaviour in fairly minor ways. However, I'm having some difficulty getting it to link reliably across different platforms. R CMD LINK seemed like it would help, but I've had difficulty finding many real-world examples online. I've

The package DICOM is a first attempt at a set of routines to import and summarize medical imaging data that conforms to the DICOM standard. This is now the industry standard for a wide variety of medical imaging equipment (e.g., PET, MRI, CT, etc.). Please see http://medical.nema.org for more information about the DICOM standard. A simple list structure holds the separate header and image

The package DICOM is a first attempt at a set of routines to import and summarize medical imaging data that conforms to the DICOM standard. This is now the industry standard for a wide variety of medical imaging equipment (e.g., PET, MRI, CT, etc.). Please see http://medical.nema.org for more information about the DICOM standard. A simple list structure holds the separate header and image

Hi, I just completed a really big rsync described earlier. Ie about 13,945 directories transfered about 600GB of data. Of 13,945 directories, 13,9441 directories transfer with matching du -b sizes of the preimage to the size of the destination machine image. of the 4 remaining directories i found source vs destination in bytes --------- a) 20480 vs 34922496 b) 28672 vs

CRAN (and crantastic) updates this week New packages ------------ * apcluster (1.0.1) Ulrich Bodenhofer http://crantastic.org/packages/apcluster The apcluster package implements Frey's and Dueck's Affinity Propagation clustering in R. The algorithms are analogous to the Matlab code published by Frey and Dueck. * BioPhysConnectoR (1.6-1) Franziska Hoffgaard