[opensuse] medical imaging software
I want to look at some MRI images from a CD the hospital sent, which expects to see a Windows box. I've decrypted the disk using J7Z and am now looking for something to view the images with. Apparently they're in DICOM format but YaST just shows me what seems to be a toolkit and a python binding. There seem to be various possible in various arcane repositories but I'm wondering if anybody else knows more about this? There's a bunch of Q&A on ubuntu sites and the general web but nothing for openSUSE specifically that I have found. TIA, Dave -- To unsubscribe, e-mail: opensuse+unsubscribe@opensuse.org To contact the owner, e-mail: opensuse+owner@opensuse.org
What does 'identify' report for the file you are trying to access? This program is part of ImageMagick. On Fri, May 18, 2018 at 1:24 PM, Dave Howorth <dave@howorth.org.uk> wrote:
I want to look at some MRI images from a CD the hospital sent, which expects to see a Windows box.
I've decrypted the disk using J7Z and am now looking for something to view the images with. Apparently they're in DICOM format but YaST just shows me what seems to be a toolkit and a python binding. There seem to be various possible in various arcane repositories but I'm wondering if anybody else knows more about this?
There's a bunch of Q&A on ubuntu sites and the general web but nothing for openSUSE specifically that I have found.
TIA, Dave
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-- Roger Oberholtzer -- To unsubscribe, e-mail: opensuse+unsubscribe@opensuse.org To contact the owner, e-mail: opensuse+owner@opensuse.org
-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi,
view the images with. Apparently they're in DICOM format but YaST just
dcim will work fine with "aeskulap" it was loong inside the "medical" repo (since years), but this year complete repo disappeared. you will find it still in: http://download.opensuse.org/repositories/home:/fstrba/openSUSE_Tumbleweed/ regards, simoN www.becherer.de -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.19 (GNU/Linux) iQIcBAEBAgAGBQJa/t1RAAoJEOuDxDCJWQG+uvUP+wUihU9S0nco4sIdeFc3JX/J 4g4XEIJ7S0W0sGXfPdP04Z9wDdAoH7tf8lnkvcTD497tTMRhM+gWIl4hb7R52clH 0cfQGmlvpJyJyG9XNlmJnjQU9kWm2hv5KecjSwM52pfBipGzVXOSIdOegh0TWSI2 45eNxDUcuKF7mB3KVscqi6Ge8TtJDccuwu8pMnNk35pCqlLzUt4YkduI7fhE7OR1 onrb62/bz3PgbifO2j83IUfjuMFiCaEll75TwXJqU81hofrRnt2AGfaTt6DbiXUj MglrSti9IGOTwb/2HVhmu9SLS7LzbBlIqvU6pSjBf24zGyQCr19o2W+YZqsIngDd 2sWAyydPQrfVzEVxtj6p2jKnvtyWavl0Fh6a+BKz9nuDxuHnx/QyNWWJEVVk/BRC A7CmXXDJLdzFu1SnSdkv2oVfMjOvi/+4cD7Qkjo4y2XAhdfAlHu/m+eNKFivgezi 91ktbm9AQmagWacVCu7JIGbzB0uRyDONaKNYOaOQRzq/JQTRRSQpdCqWlkz7bnQt OPl5NWnHOv35SspJI5+r6t3eZEq4I+OjJ7bN9wqmH7uMpcOttwOIhCGcOnyZ6Q+5 xjMg0szYVwCvEUB7GjhiiEWZX+zQLAuEUU+vLV9/ycxrX9cwv9HLiM7mx4xpMgtF LeSYZo14UDT2E0hRPxsl =Lwwx -----END PGP SIGNATURE----- -- To unsubscribe, e-mail: opensuse+unsubscribe@opensuse.org To contact the owner, e-mail: opensuse+owner@opensuse.org
On Fri, 18 May 2018 16:04:02 +0200 Simon Becherer <simon@becherer.de> wrote:
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Hi,
view the images with. Apparently they're in DICOM format but YaST just
dcim will work fine with "aeskulap"
it was loong inside the "medical" repo (since years), but this year complete repo disappeared.
you will find it still in:
http://download.opensuse.org/repositories/home:/fstrba/openSUSE_Tumbleweed/
Thanks. I just tried this first, since it's available as a 1-click install, but I haven't managed to get it to do anything useful so far. It comes up as a full-screen window; the Help menu just offers an About box, so I played with the menu entries. File/DicomDir brings up a file open dialog but when I go to the DICOMDIR file it says 'No study or bad DICOMDIR'. When I try File/Open it just goes down through the directories DICOM / ST000000 / SE000000 / and returns nothing. If I get to SE000000 in the location field and then open SE000000/MR000000 I get a completely black tab opens with the name of the study at the bottom. The website shows the last release over ten years ago, the documentation links are 404. So I'm not very impressed so far. I'll try something else. Oh, is there a way to uninstall aeskulap and the dependencies it installed and the repository it added? Ideally, a '1 click uninstall'? Cheers, Dave
regards,
simoN
www.becherer.de
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Thanks. I just tried this first, since it's available as a 1-click
Hi david, sorry, ist running fine here... and.. if know how, using is easy .... start aeskulap in full screen window go to "file / open" take care, on lower right corner you should select "any files" not "dicom files" navigate to your dicom-file-directory DO NOT USE the "dicomDir" file !!!!! instead select ALL dicom files by holding shift (or strg) and klicking on them or moving with arrow keys. if done, klick "open" (lower right) after this the fullscreen window shoudl be full with pictures. (korresponding pictures are automatically fit together) with the symbols line you could manage the arrange on screen, with mouse scrolling on a picture you could move forward and backward throu the corresponding pictures (moving through the body ;-))))). regards, simoN www.becherer.de -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.19 (GNU/Linux) iQIcBAEBAgAGBQJbABlqAAoJEOuDxDCJWQG+BrUP/RG/kqBnGLxMeobOC9wP3I5W 8CoUY+DphutzfeSKkpPUBLuaxrdHe/vs+ECNNwj4nTbg0nbiL6zj8mDN1Qnrzhqu 9CqJDH+0rvPL1haYDJu9ik4NhsruRL18j4MUFdV1+5iiWu98jKFO+aUJkI4TKAT9 chkVMBz6PTbgHnvxGmdrMBFgVeZ3tac3oexzpPdM7YikIE2dOtA+vMF5ZHjAKWEd rbMOYmdE1LshyYDbl6mK7uNwn63g9MejBausCwJjQJcb97SMphMAbufVahgyDAc6 tdo3SYvV7Axr7GSpSkaRR/AeRRF+Plg4Y6RmLbB/b+87PcPXg4vLNE6zyA34r9yp v0f870xsyz7dncltRGueY4iFPo+TnW/u1L9vusPHKoyrQqw6CpZUW+B55jCa40tB nJfHX/O0XIzO+NR0Nj3NaALdwCjZtSIRhmzsrSCPObw8h8bVlOeapStD9t9EjeoT Gk6DqrW7IvH0ykqyzVT8O9eFXN/TsHdsJPpfLzPY1TGgGVYemPIJKPKOGrUHUb5k kAjsZlEpd4A7dI2lqv4WqRkfoeRGoixnzqS56prxdWjmMIzH087GR5pw6a20P1Gh GO8JyBFe0pMlaTi3YBZOFoi42B7ejdBZdPzL07ADWuslXCcLX5STVYBBwVHeHVYa M7qSAtCw4j5QdASQ6Uzn =0O46 -----END PGP SIGNATURE----- -- To unsubscribe, e-mail: opensuse+unsubscribe@opensuse.org To contact the owner, e-mail: opensuse+owner@opensuse.org
-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Oh, by the way,, starting from commandline ist more easy: open a terminal (konsole) navigate to the directroy where you have your dicom-files (mybe ONLY dicom files, i am not shure) cd /whereever-my/dicom-files-are/ ll (only to check if they are there) aeskulap * and it will open all files in this directory and in graphical screen and you are able to slide throu it. www.becherer.de -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.19 (GNU/Linux) iQIcBAEBAgAGBQJbAB0oAAoJEOuDxDCJWQG+JxAP/2+mNeQ/ThGQvRTMr0zdd7SG P208X6hZLvC885P7Q7amwZok+Xe6XqBGG2C8JpgGPJgrz72lstGgOzds44kpNAFC M0libf2bj80q4mOlUKlnTW3VTw2C/uQu/XRSWCqMR/GZXL7c7awOFk3UtZJ19pwO Se8s3/EljLZq/3AwpznrS1dyfCgyN8tFLvex+dDmrcDBw1wdOm7P9XG3B8H9CrJz 9c85Srzv5Bg9fjjqkEevUya65OxCons2M0aZ886/+ysNLDuZJJF20hy+uZAIxQjB dZqzWezn7FIUW9xRvyaWh7cYCglqd0DNFu8LP2jDrCsq7yhGIsyhRnrX8lzJoRSb glpDI2s6vuEZg5ktWzEjqZPXAsZCYEr8rGIvjMwojMZGUi3E70El67n/4nOXuNEq l0XbDJPUgAlA2OkEW6RgVt9n6ywB/+LCPzPkLd+Ht7UhH+sQpEwh5/3Jl7SMupou 6pJcLTIY4JoQ7vyGJStKv09kJLk2hZbVxiU2YPAt7UILPsr17KjQPQq8rWp6pqCH fE8DjDHRlM2IJWyCGGSWka3j5EffQ8eQ9CxXtwkj0P2nbnfOUWQ1cT649SRGXpsi Ot4PhXc+mbMd07c/ryJNtAdZNfntDmolTDUEtxsS7/YNyt9JBNEBoGAtXKnPt0fa YhLkpaOAZN8S20IE/7T3 =VNj8 -----END PGP SIGNATURE----- -- To unsubscribe, e-mail: opensuse+unsubscribe@opensuse.org To contact the owner, e-mail: opensuse+owner@opensuse.org
On Sat, 19 May 2018 14:32:42 +0200 Simon Becherer <simon@becherer.de> wrote:
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Thanks. I just tried this first, since it's available as a 1-click
Hi david,
sorry, ist running fine here...
and.. if know how, using is easy ....
start aeskulap
in full screen window go to "file / open" take care, on lower right corner you should select "any files" not "dicom files" navigate to your dicom-file-directory
DO NOT USE the "dicomDir" file !!!!!
instead select ALL dicom files by holding shift (or strg)
The image files are in a directory hierarchy: mri-scan/DICOM/ST000000/SE0000[00-13]/MR0000[00-19] when I tried to open all from the command line, I see lots of errors like: opened file:SE000012/MR000012 E: can't load data dictionary and lots of lines like removing instance 1.3.46.670589.11.8895.5.0.6044.2018040614173196080 and the GUI window shows lots of blank panes.
and klicking on them or moving with arrow keys. if done, klick "open" (lower right)
after this the fullscreen window shoudl be full with pictures. (korresponding pictures are automatically fit together)
with the symbols line you could manage the arrange on screen,
with mouse scrolling on a picture you could move forward and backward throu the corresponding pictures (moving through the body ;-))))).
regards,
simoN
www.becherer.de -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.19 (GNU/Linux)
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On Fri, May 18, 2018 at 6:24 AM, Dave Howorth <dave@howorth.org.uk> wrote:
I want to look at some MRI images from a CD the hospital sent, which expects to see a Windows box.
I've decrypted the disk using J7Z and am now looking for something to view the images with. Apparently they're in DICOM format but YaST just shows me what seems to be a toolkit and a python binding. There seem to be various possible in various arcane repositories but I'm wondering if anybody else knows more about this?
Medical images are almost always in DICOM format. There are multiple free DICOM viewers out there, here are a couple a place to start: https://sourceforge.net/projects/opendicomviewer/ https://www.linuxlinks.com/medicalimaging/ Hope this helps, -Nick -- To unsubscribe, e-mail: opensuse+unsubscribe@opensuse.org To contact the owner, e-mail: opensuse+owner@opensuse.org
2018-05-18 8:24 GMT-03:00 Dave Howorth <dave@howorth.org.uk>:
I want to look at some MRI images from a CD the hospital sent, which expects to see a Windows box.
I've decrypted the disk using J7Z and am now looking for something to view the images with. Apparently they're in DICOM format but YaST just shows me what seems to be a toolkit and a python binding. There seem to be various possible in various arcane repositories but I'm wondering if anybody else knows more about this?
When I worked at a hospital, we used the Weasis DICOM viewer there, it is great. It is free/libre and open source software (FLOSS), multi-language, based on Java, multi-platform (runs on Windows, Linux, and Mac OS X) and can be run as a standalone / portable software, just download it from here: https://nroduit.github.io/en/getting-started/ Antonio The Linux Kamarada Project http://kamarada.github.io/ -- To unsubscribe, e-mail: opensuse+unsubscribe@opensuse.org To contact the owner, e-mail: opensuse+owner@opensuse.org
Hello, On Fri, 18 May 2018, Dave Howorth wrote:
I want to look at some MRI images from a CD the hospital sent, which expects to see a Windows box.
I've decrypted the disk using J7Z and am now looking for something to view the images with. Apparently they're in DICOM format but YaST just shows me what seems to be a toolkit and a python binding. There seem to be various possible in various arcane repositories but I'm wondering if anybody else knows more about this?
==== http://www.imagemagick.org/script/formats.php ==== DCM R Digital Imaging and Communications in Medicine (DICOM) image Used by the medical community for images like X-rays. ImageMagick sets the initial display range based on the Window Center (0028,1050) and Window Width (0028,1051) tags. Use -define dcm:display-range=reset to set the display range to the minimum and maximum pixel values. Use -define dcm:rescale=true to enable interpretation of the rescale slope and intercept settings in the file. Use -define dcm:window=centerXwidth to override the center and width settings in the file with your own values. ==== So, just try display foo.dcm or whatever the file(s) are named. HTH, -dnh -- For every rational explanation there are an infinite number of irrational explanations. -- Staples' Observation -- To unsubscribe, e-mail: opensuse+unsubscribe@opensuse.org To contact the owner, e-mail: opensuse+owner@opensuse.org
On Fri, 18 May 2018 20:23:23 +0200 David Haller <dnh@opensuse.org> wrote:
On Fri, 18 May 2018, Dave Howorth wrote:
I want to look at some MRI images from a CD the hospital sent, which expects to see a Windows box.
I've decrypted the disk using J7Z and am now looking for something to view the images with. Apparently they're in DICOM format but YaST just shows me what seems to be a toolkit and a python binding. There seem to be various possible in various arcane repositories but I'm wondering if anybody else knows more about this?
==== http://www.imagemagick.org/script/formats.php ==== DCM R Digital Imaging and Communications in Medicine (DICOM) image Used by the medical community for images like X-rays. ImageMagick sets the initial display range based on the Window Center (0028,1050) and Window Width (0028,1051) tags. Use -define dcm:display-range=reset to set the display range to the minimum and maximum pixel values. Use -define dcm:rescale=true to enable interpretation of the rescale slope and intercept settings in the file. Use -define dcm:window=centerXwidth to override the center and width settings in the file with your own values. ====
So, just try
display foo.dcm
or whatever the file(s) are named.
HTH, -dnh
Thanks to one and all. That works and shows me an individual image, David, which is a good start. What I'm really looking for is something that will let me step through the sequence of images, and display multiple images. And for Roger: $ identify DICOM/ST000000/SE000000/MR000007 DICOM/ST000000/SE000000/MR000007 DCM 320x320 320x320+0+0 8-bit sRGB 216KB 0.000u 0:00.000 Simon, Nick & Antonio. Thanks for those pointers. They rather leave me in the same position as before, in that I'll have to try various options and see what works. I was hoping there might be a consensus. -- To unsubscribe, e-mail: opensuse+unsubscribe@opensuse.org To contact the owner, e-mail: opensuse+owner@opensuse.org
Hello, On Sat, 19 May 2018, Dave Howorth wrote:
David Haller <dnh@opensuse.org> wrote:
So, just try
display foo.dcm
or whatever the file(s) are named.
Thanks to one and all. That works and shows me an individual image, David, which is a good start. What I'm really looking for is something that will let me step through the sequence of images, and display multiple images.
And for Roger:
$ identify DICOM/ST000000/SE000000/MR000007 DICOM/ST000000/SE000000/MR000007 DCM 320x320 320x320+0+0 8-bit sRGB 216KB 0.000u 0:00.000
Try hitting F1 in display, that shows a dialog with the keys... E.g. "space" ("if the images is a multi-paged document...") Oh, and BTW: gimp can handle DICOM too, probably imports them as layers (similar to an animated gif) if there are multiple images. You could then try to convert to e.g. (multipage) tiff or into whatever single-image format. HTH, -dnh -- /* panic?? These should never occur in our application. */ linux-2.6.6/drivers/scsi/aic7xxx/aiclib.c -- To unsubscribe, e-mail: opensuse+unsubscribe@opensuse.org To contact the owner, e-mail: opensuse+owner@opensuse.org
On Sat, 19 May 2018 05:43:02 +0200 David Haller <dnh@opensuse.org> wrote:
Hello,
On Sat, 19 May 2018, Dave Howorth wrote:
David Haller <dnh@opensuse.org> wrote:
So, just try
display foo.dcm
or whatever the file(s) are named.
Thanks to one and all. That works and shows me an individual image, David, which is a good start. What I'm really looking for is something that will let me step through the sequence of images, and display multiple images.
And for Roger:
$ identify DICOM/ST000000/SE000000/MR000007 DICOM/ST000000/SE000000/MR000007 DCM 320x320 320x320+0+0 8-bit sRGB 216KB 0.000u 0:00.000
Try hitting F1 in display, that shows a dialog with the keys...
E.g. "space" ("if the images is a multi-paged document...")
Oh, and BTW: gimp can handle DICOM too, probably imports them as layers (similar to an animated gif) if there are multiple images. You could then try to convert to e.g. (multipage) tiff or into whatever single-image format.
Thanks. I'm hoping to find something a bit more purpose-designed and intuitive.
HTH, -dnh
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On 05/18/2018 06:24 AM, Dave Howorth wrote:
I want to look at some MRI images from a CD the hospital sent, which expects to see a Windows box.
I've decrypted the disk using J7Z and am now looking for something to view the images with. Apparently they're in DICOM format but YaST just shows me what seems to be a toolkit and a python binding. There seem to be various possible in various arcane repositories but I'm wondering if anybody else knows more about this?
There's a bunch of Q&A on ubuntu sites and the general web but nothing for openSUSE specifically that I have found.
TIA, Dave
Getting old are we.... KDE3 always packaged http://sourceforge.net/projects/xmedcon/files/ which was a good medical imaging reading package. I don't know how current it is, but I routinely built it a couple of years back for TDE. -- David C. Rankin, J.D.,P.E. -- To unsubscribe, e-mail: opensuse+unsubscribe@opensuse.org To contact the owner, e-mail: opensuse+owner@opensuse.org
On 05/18/2018 09:32 PM, David C. Rankin wrote:
KDE3 always packaged http://sourceforge.net/projects/xmedcon/files/ which was a good medical imaging reading package. I don't know how current it is, but I routinely built it a couple of years back for TDE.
Surprisingly this is still a very active project with latest release in April. I provides source, rpm, and windows installs. Who'd a thunk.. -- David C. Rankin, J.D.,P.E. -- To unsubscribe, e-mail: opensuse+unsubscribe@opensuse.org To contact the owner, e-mail: opensuse+owner@opensuse.org
participants (7)
-
Dave Howorth -
David C. Rankin -
David Haller -
Linux Kamarada -
Nick LeRoy -
Roger Oberholtzer -
Simon Becherer