On Mon, 17 Jul 2017, Mathieu Malaterre wrote: > On Mon, Jul 17, 2017 at 4:46 PM, Yaroslav Halchenko <y...@debian.org> wrote:
> > On Mon, 17 Jul 2017, Mathieu Malaterre wrote: > >> > sorry... could you please provide a complete tiny "script" since in the > >> > above list of steps I just see > >> > cp ~/buggy.dcm bug2/jpeg.dcm > >> > and I see no way to get buggy.dcm and you did say that it worked fine on > >> > that downloaded SIEMENS_MOSAIC_12BitsStored-16BitsJPEG.dcm* > >> What I tried to say is: > >> $ cp SIEMENS_MOSAIC_12BitsStored-16BitsJPEG.dcm ~/buggy.dcm > >> does reproduce the symptoms (you'll see the error on your end). > >> Let me know if this still does not make sense, and I'll try to write a > >> tiny script otherwise. > > someone needs to write it one way or another and I would > > appreciate if you do it ;) trying to undig myself from TODOs here > % cat tiny.sh > #!/bin/sh -x > pushd /tmp > wget -O buggy.dcm > "https://sourceforge.net/p/gdcm/gdcmdata/ci/master/tree/SIEMENS_MOSAIC_12BitsStored-16BitsJPEG.dcm?format=raw"; > mkdir bug1 > mkdir bug2 > mkdir demo > cp buggy.dcm bug1 > gdcmconv --raw buggy.dcm bug2/raw.dcm > nib-dicomfs /tmp/bug1 /tmp/demo & > sleep 5 > find /tmp/demo > sudo umount /tmp/demo > nib-dicomfs /tmp/bug2 /tmp/demo & > sleep 5 > find /tmp/demo > popd sorry -- still doesn't reproduce (did just minor changes to your script so I could rerun it) $> cat tiny.sh #!/bin/bash -x pushd /tmp rm -rf buggy.dcm bug1 bug2 demo wget -O buggy.dcm "https://sourceforge.net/p/gdcm/gdcmdata/ci/master/tree/SIEMENS_MOSAIC_12BitsStored-16BitsJPEG.dcm?format=raw"; mkdir bug1 mkdir bug2 mkdir demo cp buggy.dcm bug1 gdcmconv --raw buggy.dcm bug2/raw.dcm nib-dicomfs /tmp/bug1 /tmp/demo & sleep 5 find /tmp/demo sudo umount /tmp/demo nib-dicomfs /tmp/bug2 /tmp/demo & sleep 5 find /tmp/demo sudo umount /tmp/demo popd $> ./tiny.sh + pushd /tmp /tmp ~/trash + rm -rf buggy.dcm bug1 bug2 demo + wget -O buggy.dcm 'https://sourceforge.net/p/gdcm/gdcmdata/ci/master/tree/SIEMENS_MOSAIC_12BitsStored-16BitsJPEG.dcm?format=raw' --2017-07-17 11:34:51-- https://sourceforge.net/p/gdcm/gdcmdata/ci/master/tree/SIEMENS_MOSAIC_12BitsStored-16BitsJPEG.dcm?format=raw Resolving sourceforge.net (sourceforge.net)... 216.34.181.60 Connecting to sourceforge.net (sourceforge.net)|216.34.181.60|:443... connected. HTTP request sent, awaiting response... 200 OK Length: unspecified [application/dicom] Saving to: ‘buggy.dcm’ buggy.dcm [ <=> ] 128.31K --.-KB/s in 0.06s 2017-07-17 11:34:52 (2.14 MB/s) - ‘buggy.dcm’ saved [131390] + mkdir bug1 + mkdir bug2 + mkdir demo + cp buggy.dcm bug1 + gdcmconv --raw buggy.dcm bug2/raw.dcm + sleep 5 + nib-dicomfs /tmp/bug1 /tmp/demo + find /tmp/demo /tmp/demo /tmp/demo/xxxx^xxxxxxx^R /tmp/demo/xxxx^xxxxxxx^R/INFO /tmp/demo/xxxx^xxxxxxx^R/20080807_101152 /tmp/demo/xxxx^xxxxxxx^R/20080807_101152/INFO /tmp/demo/xxxx^xxxxxxx^R/20080807_101152/18 /tmp/demo/xxxx^xxxxxxx^R/20080807_101152/18/INFO /tmp/demo/xxxx^xxxxxxx^R/20080807_101152/18/18.png /tmp/demo/xxxx^xxxxxxx^R/20080807_101152/18/18.nii + sudo umount /tmp/demo + sleep 5 + nib-dicomfs /tmp/bug2 /tmp/demo + find /tmp/demo /tmp/demo /tmp/demo/xxxx^xxxxxxx^R /tmp/demo/xxxx^xxxxxxx^R/INFO /tmp/demo/xxxx^xxxxxxx^R/20080807_101152 /tmp/demo/xxxx^xxxxxxx^R/20080807_101152/INFO /tmp/demo/xxxx^xxxxxxx^R/20080807_101152/18 /tmp/demo/xxxx^xxxxxxx^R/20080807_101152/18/INFO /tmp/demo/xxxx^xxxxxxx^R/20080807_101152/18/18.png /tmp/demo/xxxx^xxxxxxx^R/20080807_101152/18/18.nii + sudo umount /tmp/demo + popd ~/trash hopa:~/trash $> welp dicom PATH : /usr/lib/python2.7/dist-packages/dicom/__init__.pyc SRC PATH : /usr/lib/python2.7/dist-packages/dicom/__init__.py VERSION : Not found __version__: '0.9.9' PACKAGE : python-dicom ii python-dicom 0.9.9-2 all DICOM medical file reading and writing (Python 2) python-dicom: Installed: 0.9.9-2 Candidate: 0.9.9-2 Version table: *** 0.9.9-2 600 100 http://http.debian.net/debian stretch/main amd64 Packages 100 http://http.debian.net/debian stretch/main i386 Packages 600 http://http.debian.net/debian sid/main amd64 Packages 600 http://http.debian.net/debian sid/main i386 Packages 100 /var/lib/dpkg/status 0.9.9-1~nd80+1+nd90+1 500 500 http://neuro.debian.net/debian stretch/main amd64 Packages 500 http://neuro.debian.net/debian stretch/main i386 Packages $> welp nibabel PATH : /usr/lib/python2.7/dist-packages/nibabel/__init__.pyc SRC PATH : /usr/lib/python2.7/dist-packages/nibabel/__init__.py VERSION : 2.1.0 __version__: '2.1.0' PACKAGE : python-nibabel ii python-nibabel 2.1.0-1 all Python bindings to various neuroimaging data formats python-nibabel: Installed: 2.1.0-1 Candidate: 2.1.0-1 Version table: *** 2.1.0-1 600 100 http://http.debian.net/debian stretch/main amd64 Packages 100 http://http.debian.net/debian stretch/main i386 Packages 600 http://http.debian.net/debian sid/main amd64 Packages 600 http://http.debian.net/debian sid/main i386 Packages 100 /var/lib/dpkg/status 2.1.0-1~nd90+1 500 500 http://neuro.debian.net/debian stretch/main amd64 Packages 500 http://neuro.debian.net/debian stretch/main i386 Packages -- Yaroslav O. Halchenko Center for Open Neuroscience http://centerforopenneuroscience.org Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419 WWW: http://www.linkedin.com/in/yarik
