Hi, I saw that nifti file support was currently in the pipeline. If the license issue is solved, I can provide you a nifticlib.i file that is compatible with C89 compilers (the converted file needs a C99 compiler, so compiling it with MSVC is not possible), as I've done this for my hobbies some weeks ago. Matthieu
On 9/30/07, Matthieu Brucher <matthieu.brucher@gmail.com> wrote:
I saw that nifti file support was currently in the pipeline. If the license issue is solved, I can provide you a nifticlib.i file that is compatible with C89 compilers (the converted file needs a C99 compiler, so compiling it with MSVC is not possible), as I've done this for my hobbies some weeks ago.
Hey Matthieu, The pynifti license issue has been resolved. Michael Hanke, the author, has released his software under an MIT license: http://sourceforge.net/project/shownotes.php?group_id=126549&release_id=543252 Early this week, Chris Burns and I will check this code into the SciPy repository. Once we do, it would be great if you could either integrate your nifticlib.i into the codebase or just send us your code. Thanks, -- Jarrod Millman Computational Infrastructure for Research Labs 10 Giannini Hall, UC Berkeley phone: 510.643.4014 http://cirl.berkeley.edu/
Excellent news !! Matthieu 2007/10/1, Jarrod Millman <millman@berkeley.edu>:
I saw that nifti file support was currently in the pipeline. If the
On 9/30/07, Matthieu Brucher <matthieu.brucher@gmail.com> wrote: license
issue is solved, I can provide you a nifticlib.i file that is compatible with C89 compilers (the converted file needs a C99 compiler, so compiling it with MSVC is not possible), as I've done this for my hobbies some weeks ago.
Hey Matthieu,
The pynifti license issue has been resolved. Michael Hanke, the author, has released his software under an MIT license:
http://sourceforge.net/project/shownotes.php?group_id=126549&release_id=543252
Early this week, Chris Burns and I will check this code into the SciPy repository. Once we do, it would be great if you could either integrate your nifticlib.i into the codebase or just send us your code.
Thanks,
-- Jarrod Millman Computational Infrastructure for Research Labs 10 Giannini Hall, UC Berkeley phone: 510.643.4014 http://cirl.berkeley.edu/ _______________________________________________ Scipy-dev mailing list Scipy-dev@scipy.org http://projects.scipy.org/mailman/listinfo/scipy-dev
I would like to put in my two-cents worth regarding the nifti format. I wrote a library in python that handles dicom, afni, and nifti format with the appropriate conversions between coordinate systems. The goal was to be able to script FSL, AFNI, SPM and our in-house python code without doing a file conversion at every step. Unfortunately, AFNI defines the quaternion transformation relative to LPI coordinates, while FSL defines it as going to RAI. I don't know how SPM does it - we are still in the process of scripting that. The result is that either the fans of fslview or the fans of AFNI are upset about any given solution. I don't know if this is covered elsewhere or not, but it should receive some attention. John p.s. I would contribute the code if anyone is interested. I completely rewrote the mess that I offered last spring, and it is probably respectable python code now although it could stand being refactored again. On 10/1/07, Matthieu Brucher <matthieu.brucher@gmail.com> wrote:
Excellent news !!
Matthieu
2007/10/1, Jarrod Millman <millman@berkeley.edu>:
I saw that nifti file support was currently in the pipeline. If the
On 9/30/07, Matthieu Brucher <matthieu.brucher@gmail.com> wrote: license
issue is solved, I can provide you a nifticlib.i file that is compatible with C89 compilers (the converted file needs a C99 compiler, so compiling it with MSVC is not possible), as I've done this for my hobbies some weeks ago.
Hey Matthieu,
The pynifti license issue has been resolved. Michael Hanke, the author, has released his software under an MIT license:
http://sourceforge.net/project/shownotes.php?group_id=126549&release_id=543252
Early this week, Chris Burns and I will check this code into the SciPy repository. Once we do, it would be great if you could either integrate your nifticlib.i into the codebase or just send us your code.
Thanks,
-- Jarrod Millman Computational Infrastructure for Research Labs 10 Giannini Hall, UC Berkeley phone: 510.643.4014 http://cirl.berkeley.edu/ _______________________________________________ Scipy-dev mailing list Scipy-dev@scipy.org http://projects.scipy.org/mailman/listinfo/scipy-dev
_______________________________________________ Scipy-dev mailing list Scipy-dev@scipy.org http://projects.scipy.org/mailman/listinfo/scipy-dev
-- John Ollinger University of Wisconsin Waisman Center, T233 1500 Highland Ave Madison, WI 53711 http://brainimaging.waisman.wisc.edu/~jjo/
Hey John, Please send me the new version of your code. The nifti code that has been checked in uses niftilib, the official reference implementation of nifti that all the major packages are using. The python wrapper is the official implementation as well. Once we get the build issues sorted out, it would be great if you would be willing to test out the code. If there are any issues that it doesn't get right, we should get them fixed upstream. Thanks, -- Jarrod Millman Computational Infrastructure for Research Labs 10 Giannini Hall, UC Berkeley phone: 510.643.4014 http://cirl.berkeley.edu/
Jarrod, I'll send you the code (probably tomorrow - I'm writing a chunk of grant proposal today). I would be happy to test the new code. The unit tests I wrote for my own code can be easily adapted. John On 10/4/07, Jarrod Millman <millman@berkeley.edu> wrote:
Hey John,
Please send me the new version of your code. The nifti code that has been checked in uses niftilib, the official reference implementation of nifti that all the major packages are using. The python wrapper is the official implementation as well. Once we get the build issues sorted out, it would be great if you would be willing to test out the code. If there are any issues that it doesn't get right, we should get them fixed upstream.
Thanks,
-- Jarrod Millman Computational Infrastructure for Research Labs 10 Giannini Hall, UC Berkeley phone: 510.643.4014 http://cirl.berkeley.edu/ _______________________________________________ Scipy-dev mailing list Scipy-dev@scipy.org http://projects.scipy.org/mailman/listinfo/scipy-dev
-- John Ollinger University of Wisconsin Waisman Center, T233 1500 Highland Ave Madison, WI 53711 http://brainimaging.waisman.wisc.edu/~jjo/
Hi, Here is the nifticlib.i file, not a lot of differences. I would like to put in my two-cents worth regarding the nifti format. I
wrote a library in python that handles dicom, afni, and nifti format with the appropriate conversions between coordinate systems.
Are you able to read DTI image files in DICOM ? That could interest me a lot. The goal was to be able to script FSL, AFNI, SPM and our in-house python
code without doing a file conversion at every step.
Do you have a wrapper over FSL and SPM in Python ? Unfortunately, AFNI defines the quaternion transformation relative to LPI
coordinates, while FSL defines it as going to RAI. I don't know how SPM does it - we are still in the process of scripting that. The result is that either the fans of fslview or the fans of AFNI are upset about any given solution.
We have the same problem when converting DICOM to analyze, the two pieces of software we use (MRIConvert and MRICRO or something like that) don't use the same coordinate system... I don't know if this is covered elsewhere or not, but it should receive some
attention.
You have mine :) Matthieu
Hi, It should read DTI images, but I have only tested it on GE scanners. The code does support Siemens scanners, so it wouldn't take much to get it to work. I did not wrap FSL or SPM. I am not sure how to wrap programs written in matlab. Other than to use matlab itself. The code return a 4x4 transformation matrix that takes the raw data into RAI coordinates. It doesn't do anything to the data itself. I will put the code and some documentation (yet to be written) on my home page, probably tomorrow but maybe Saturday. John On 10/4/07, Matthieu Brucher <matthieu.brucher@gmail.com> wrote:
Hi,
Here is the nifticlib.i file, not a lot of differences.
I would like to put in my two-cents worth regarding the nifti format. I
wrote a library in python that handles dicom, afni, and nifti format with the appropriate conversions between coordinate systems.
Are you able to read DTI image files in DICOM ? That could interest me a lot.
The goal was to be able to script FSL, AFNI, SPM and our in-house python
code without doing a file conversion at every step.
Do you have a wrapper over FSL and SPM in Python ?
Unfortunately, AFNI defines the quaternion transformation relative to LPI
coordinates, while FSL defines it as going to RAI. I don't know how SPM does it - we are still in the process of scripting that. The result is that either the fans of fslview or the fans of AFNI are upset about any given solution.
We have the same problem when converting DICOM to analyze, the two pieces of software we use (MRIConvert and MRICRO or something like that) don't use the same coordinate system...
I don't know if this is covered elsewhere or not, but it should receive
some attention.
You have mine :)
Matthieu
_______________________________________________ Scipy-dev mailing list Scipy-dev@scipy.org http://projects.scipy.org/mailman/listinfo/scipy-dev
-- John Ollinger University of Wisconsin Waisman Center, T233 1500 Highland Ave Madison, WI 53711 http://brainimaging.waisman.wisc.edu/~jjo/
participants (3)
-
Jarrod Millman -
John Ollinger -
Matthieu Brucher