On Thu, 13 Jul 2017, Mathieu Malaterre wrote: > Step: > $ cd /tmp > $ wget > "https://sourceforge.net/p/gdcm/gdcmdata/ci/master/tree/SIEMENS_MOSAIC_12BitsStored-16BitsJPEG.dcm?format=raw"; > $ mkdir bug > $ gdcmconv --raw SIEMENS_MOSAIC_12BitsStored-16BitsJPEG.dcm* bug/raw.dcm > $ nib-dicomfs /tmp/bug /tmp/demo
> In another shell: > $ find /tmp/demo/ Great -- thanks! but seems to work for me just fine so -- first tried with most recent devel of nibabel and pydicom -- worked... (see below II.). Then tried with the ones installed -- also worked (I.) (welp is my command you could find at http://git.onerussian.com/?p=etc/bash.git;a=blob;f=.bash/bashrc/30_aliases_sh;h=28fa4ad215839110953f598becbbbd586ff8edb0;hb=HEAD#l1009 if interested) I. $> which nib-dicomfs /usr/bin/nib-dicomfs 2 27593.....................................:Thu 13 Jul 2017 11:29:48 AM EDT:. hopa:/tmp $> 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 2 27594.....................................:Thu 13 Jul 2017 11:29:54 AM EDT:. hopa:/tmp $> 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 2 27595.....................................:Thu 13 Jul 2017 11:29:58 AM EDT:. hopa:/tmp $> nib-dicomfs /tmp/bug /tmp/demo & [1] 8114 2 27596 [1].....................................:Thu 13 Jul 2017 11:30:04 AM EDT:. hopa:/tmp $> 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 II. $> virtualenv --system-site-packages test-dicom Running virtualenv with interpreter /usr/bin/python2 New python executable in /tmp/test-dicom/bin/python2 Also creating executable in /tmp/test-dicom/bin/python Installing setuptools, pkg_resources, pip, wheel...done. 2 27576.....................................:Thu 13 Jul 2017 11:25:43 AM EDT:. hopa:/tmp $> source test-dicom/bin/activate (test-dicom) 2 27577.....................................:Thu 13 Jul 2017 11:25:48 AM EDT:. hopa:/tmp $> pip install --upgrade git+https://github.com/darcymason/pydicom/ Collecting git+https://github.com/darcymason/pydicom/ Cloning https://github.com/darcymason/pydicom/ to ./pip-_KHMlx-build Installing collected packages: pydicom Found existing installation: pydicom 0.9.9 Not uninstalling pydicom at /usr/lib/python2.7/dist-packages, outside environment /tmp/test-dicom Running setup.py install for pydicom ... done Successfully installed pydicom-1.0.0a1 (test-dicom) 2 27578.....................................:Thu 13 Jul 2017 11:26:03 AM EDT:. hopa:/tmp $> pip install --upgrade git+https://github.com/nipy/nibabel Collecting git+https://github.com/nipy/nibabel Cloning https://github.com/nipy/nibabel to ./pip-90D2wS-build Installing collected packages: nibabel Found existing installation: nibabel 2.1.0 Not uninstalling nibabel at /usr/lib/python2.7/dist-packages, outside environment /tmp/test-dicom Running setup.py install for nibabel ... done Successfully installed nibabel-2.2.0.dev0 pip install --upgrade git+https://github.com/nipy/nibabel 10.36s user 2.28s system 22% cpu 56.005 total (test-dicom) 2 27579.....................................:Thu 13 Jul 2017 11:27:10 AM EDT:. hopa:/tmp $> wget "https://sourceforge.net/p/gdcm/gdcmdata/ci/master/tree/SIEMENS_MOSAIC_12BitsStored-16BitsJPEG.dcm?format=raw"; --2017-07-13 11:27:23-- 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: ‘SIEMENS_MOSAIC_12BitsStored-16BitsJPEG.dcm?format=raw’ SIEMENS_MOSAIC_12Bit [ <=> ] 128.31K --.-KB/s in 0.1s 2017-07-13 11:27:23 (879 KB/s) - ‘SIEMENS_MOSAIC_12BitsStored-16BitsJPEG.dcm?format=raw’ saved [131390] (test-dicom) 2 27580.....................................:Thu 13 Jul 2017 11:27:24 AM EDT:. hopa:/tmp $> mkdir bug (test-dicom) 2 27581.....................................:Thu 13 Jul 2017 11:27:28 AM EDT:. hopa:/tmp $> gdcmconv --raw SIEMENS_MOSAIC_12BitsStored-16BitsJPEG.dcm* bug/raw.dcm (test-dicom) 2 27582.....................................:Thu 13 Jul 2017 11:27:35 AM EDT:. hopa:/tmp $> nib-dicomfs /tmp/bug /tmp/demo fuse: bad mount point `/tmp/demo': No such file or directory (test-dicom) 2 27583 ->1.....................................:Thu 13 Jul 2017 11:27:45 AM EDT:. hopa:/tmp $> mkdir demo (test-dicom) 2 27584.....................................:Thu 13 Jul 2017 11:27:53 AM EDT:. hopa:/tmp $> nib-dicomfs /tmp/bug /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 > Cheers -- 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
