Is it straight off the scanner? It does not have the siemens ascii
header which usually means that it has been manipulated in some way. You
can try using mri_convert with --it dicom
doug





On 05/23/2013 12:57 PM, Cat Chong wrote:
> no it has not.
>
>
> ------------------------------------------------------------------------
> *From:* Douglas N Greve <greve@nmr.mgh.harvard.edu>
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Sent:* Thursday, May 23, 2013 9:43 AM
> *Subject:* Re: [Freesurfer] Siemens dicom error on mri_convert
>
> has this file been anonymized?
> On 05/23/2013 12:39 PM, Cat Chong wrote:
> > Hello Experts,
> > I am trying to run the mri_convert command prior to the recon-all
> > command on Siemens T1 dicoms (as suggested in the archives). I am
> > using freesurfer version: freesurfer-Darwin-lion-stable-pub-v5.3.0,
> > Mac OS X Lion 10.7.5
> > I am using the command below:
> > mri_convert -it siemens_dicom -ot mgz 1002/IM-0001-0001.dcm 2001.mgz
> > Below is the command line error I receive, it is a similar error I
> > receive when I try to use the command recon-all on the Siemens dicoms.
> > I have used freesurfer before on GE dicoms and never had a problem
> > running recon-all. Is this error message particular to the Siemens
> > dicoms, and would you be able to tell me how to proceed?
> > Thank you very much for you help,
> > Cat
> > reading from 1002/IM-0001-0001.dcm...
> > Getting Series No
> > Scanning Directory
> > INFO: Found 130 files in 1002
> > INFO: Scanning for Series Number 2
> > INFO: found 128 files in series
> > INFO: loading series header info.
> > INFO: sorting.
> > RunNo = 1
> > WARNING: Run 1 appears to be truncated
> >  Files Found: 128, Files Expected (lRep+1): 1
> > FileName 1002/IM-0001-0001.dcm
> > Identification
> >            NumarisVer        syngo MR D11
> >            ScannerModel      Skyra
> >            PatientName RS-FMRI^RS-FMRI
> > Date and time
> >            StudyDate        20130222
> >            StudyTime 082109.140000
> >            SeriesTime 082812.906000
> >            AcqTime 082237.315000
> > Acquisition parameters
> >            PulseSeq *tfl3d1_16ns
> >            Protocol          SAG MP Rage
> >            PhEncDir          ROW
> >            EchoNo            1
> >            FlipAngle        8
> >            EchoTime          3.03
> >            InversionTime    1000
> >            RepetitionTime    2400
> >            PhEncFOV          0
> >            ReadoutFOV        0
> > Image information
> >            RunNo            1
> >            SeriesNo          2
> >            ImageNo          1
> >            NImageRows        256
> >            NImageCols        256
> >            NFrames          128
> >            SliceArraylSize  0
> >            IsMosaic          1
> >            ImgPos            -78.6002 128.0000 93.1332
> >            VolRes 1.0000  1.0000 1.2500
> >            VolDim 0        0 0
> >            Vc                -0.0000 -1.0000 0.0000
> >            Vr                -0.0000 -0.0000 -1.0000
> >            Vs 0.0000  0.0000 0.0000
> >            VolCenter 0.0000  0.0000 0.0000
> >            TransferSyntaxUID 1.2.840.10008.1.2.1
> > WARNING: file 1002/IM-0001-0001.dcm does not contain a Siemens ASCII
> > header
> > has this file been anonymized?
> > ERROR: cannot unpack mosiacs without ASCII header
> >
> >
> > _______________________________________________
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>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
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>
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>
>
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/