Hi,
I am trying to convert from dicom to mgz (or nii) in Freesurfer by using dicom files as the one attached to this message. However, Freesurfer reports that this file is not a dicom. It seems weird to me since it can be opened with MRIcro, SPM as dicom, but not with Freesurfer. Could anyone tell me if there is another Freesurfer command to covert these dicoms to mgz from the command line?
Thanks in advance.
Best, Jose --- Jose Luis Cantero, Ph.D. Laboratory of Functional Neuroscience Department of Physiology, Anatomy, and Cell Biology University Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Sevilla - Spain -
Phone: +34 954 977433 Fax: +34 954 349151 Email: jlcanlor@upo.es http://www.upo.es/neuroaging/en/
Pablo This Dicom you attached comes from a Philips scanner. We had a bug in 3 Philips scanners with their DICOM files not being compliant with DICOM standard.
In your header there's "DICOM 4.0 MR datadefs" - that's the problem with Philips: Dicom current standard is 3.
Take a look of this thread: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg08397.html http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg08397.html ----------------------------------------------------------- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom --- Novo Netfilter 3.0 www.Netfilter.com.br --- Em breve Netfilter Small Business
2009/7/17 Jose Luis Cantero Lorente jlcanlor@upo.es
Hi,
I am trying to convert from dicom to mgz (or nii) in Freesurfer by using dicom files as the one attached to this message. However, Freesurfer reports that this file is not a dicom. It seems weird to me since it can be opened with MRIcro, SPM as dicom, but not with Freesurfer. Could anyone tell me if there is another Freesurfer command to covert these dicoms to mgz from the command line?
Thanks in advance.
Best, Jose
Jose Luis Cantero, Ph.D. Laboratory of Functional Neuroscience Department of Physiology, Anatomy, and Cell Biology University Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Sevilla
- Spain -
Phone: +34 954 977433 Fax: +34 954 349151 Email: jlcanlor@upo.es http://www.upo.es/neuroaging/en/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
we often have problems reading philips dicoms, not sure why.
doug
On Fri, 17 Jul 2009, Jose Luis Cantero Lorente wrote:
Hi,
I am trying to convert from dicom to mgz (or nii) in Freesurfer by using dicom files as the one attached to this message. However, Freesurfer reports that this file is not a dicom. It seems weird to me since it can be opened with MRIcro, SPM as dicom, but not with Freesurfer. Could anyone tell me if there is another Freesurfer command to covert these dicoms to mgz from the command line?
Thanks in advance.
Best, Jose
Jose Luis Cantero, Ph.D. Laboratory of Functional Neuroscience Department of Physiology, Anatomy, and Cell Biology University Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Sevilla
- Spain -
Phone: +34 954 977433 Fax: +34 954 349151 Email: jlcanlor@upo.es http://www.upo.es/neuroaging/en/
Guys,
I am using Philips DICOMs from INTERA and ACHIEVA generation systems without any problems. So far I have done about 600 analyses. INTERAs are on 11.4 software version and ACHIEVAs went from release 2 up to the current 2.6.1 (and soon release 3)
However the images do not go directly from the scanner (export to DICOM files). Instead They go from the PACS to OsiriX (dcmtk) to dcmtk. The last one stores them on a disc where FreeSurfer finds them.
Best
On Fri, Jul 17, 2009 at 3:27 PM, Doug Greve greve@nmr.mgh.harvard.eduwrote:
we often have problems reading philips dicoms, not sure why.
doug
On Fri, 17 Jul 2009, Jose Luis Cantero Lorente wrote:
Hi,
I am trying to convert from dicom to mgz (or nii) in Freesurfer by using dicom files as the one attached to this message. However, Freesurfer reports that this file is not a dicom. It seems weird to me since it can be opened with MRIcro, SPM as dicom, but not with Freesurfer. Could anyone tell me if there is another Freesurfer command to covert these dicoms to mgz from the command line?
Thanks in advance.
Best, Jose
Jose Luis Cantero, Ph.D. Laboratory of Functional Neuroscience Department of Physiology, Anatomy, and Cell Biology University Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Sevilla
- Spain -
Phone: +34 954 977433 Fax: +34 954 349151 Email: jlcanlor@upo.es http://www.upo.es/neuroaging/en/
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Because Philips Dicoms are not true Dicoms At least here in Brazil they told us they are aware of the problem and suggest we export in nii format ----------------------------------------------------------- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom --- Novo Netfilter 3.0 www.Netfilter.com.br --- Em breve Netfilter Small Business
2009/7/17 Doug Greve greve@nmr.mgh.harvard.edu
we often have problems reading philips dicoms, not sure why.
doug
On Fri, 17 Jul 2009, Jose Luis Cantero Lorente wrote:
Hi,
I am trying to convert from dicom to mgz (or nii) in Freesurfer by using dicom files as the one attached to this message. However, Freesurfer reports that this file is not a dicom. It seems weird to me since it can be opened with MRIcro, SPM as dicom, but not with Freesurfer. Could anyone tell me if there is another Freesurfer command to covert these dicoms to mgz from the command line?
Thanks in advance.
Best, Jose
Jose Luis Cantero, Ph.D. Laboratory of Functional Neuroscience Department of Physiology, Anatomy, and Cell Biology University Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Sevilla
- Spain -
Phone: +34 954 977433 Fax: +34 954 349151 Email: jlcanlor@upo.es http://www.upo.es/neuroaging/en/
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Doug Greve -
Jose Luis Cantero Lorente -
Martin Kavec -
Pedro Paulo de Magalhães Oliveira Junior