Dear Doug
Yes, the data is straight off the scanner, I don't think it has been
manipulated, but I will check.
When I run the the command suggested I get the below error message:
mri_convert –it dicom -ot mgz 1002/IM-0001-0001.dcm 1002.mgz
mri_convert –it dicom -ot mgz 1002/IM-0001-0001.dcm 1002.mgz
mri_convert: extra arguments ("1002/IM-0001-0001.dcm" and following)
type mri_convert -u for usage
I am not quite sure where I am making an error.
Cat
________________________________
From: Douglas N Greve <gr...@nmr.mgh.harvard.edu>
To: Cat Chong <cavecreekcut...@yahoo.com>; "Freesurfer@nmr.mgh.harvard.edu"
<Freesurfer@nmr.mgh.harvard.edu>
Sent: Thursday, May 23, 2013 10:06 AM
Subject: Re: [Freesurfer] Siemens dicom error on mri_convert
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 <gr...@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
> >
> >
> > _______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu <mailto:gr...@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/
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom
> it is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline
> <http://www.partners.org/complianceline>. If the e-mail was sent to
> you in error
> but does not contain patient information, please contact the sender
> and properly
> dispose of the e-mail.
>
>
>
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@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/_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
