Hi Paige,
I ran into a similar problem a few months ago. Freesurfer 3.0.5 could not read
data from a TIM trio with numaris B17. I solved this by transplanting (copying)
a number of files from freesurfer 4.4.0 (the recent one at the time) into
3.0.5. unpacsdcmdir, mri_convert and a few more, that worked okay, but I since
switched to freesurfer 4.5.0 for good. If you have to stick to 3.0.3 I can try
to look up which files I had to replace in 3.0.5. Or alternatively you can
install v4.5.0 parallel to 3.0.3 and only use it to import the DICOM data...
best regards
Sebastian
On Mar 19, 2010, at 12:37 PM, freesurfer-requ...@nmr.mgh.harvard.edu wrote:
> Message: 7
> Date: Fri, 19 Mar 2010 14:37:24 -0500
> From: Paige Scalf <psc...@gmail.com>
> Subject: [Freesurfer] trio dicom files and mri_convert
> To: freesurfer@nmr.mgh.harvard.edu
> Message-ID:
> <1113e70c1003191237y6f5723aeha927124dd30b5...@mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hello,
>
> I've been trying to use mri_convert
> (freesurfer-Darwin-tiger-stable-pub-v3.0.3) to reconstruct images from our
> Siemens Magnetom Trio. When I type:
>
> mri_convert -it siemens_dicom -ot analyze4d DB_A0A1_318.MR.BECK-PAIGE_
> A0A1_INHABITION.0003.0001.2010.03.18.16.34.50.500000.21615932.IMA Block1.img
>
>
> DB*.IMA and Block1.img are the input and output files respectively, I get
> the output detailed below (the salient error seems to be that mri_convert
> can't find a useful transformation matrix).
>
> Can you tell me what I can do to correct this problem?
> Many thanks in advance,
>
> Paige Scalf
>
>
> mri_convert -it siemens_dicom -ot analyze4d
> DB_A0A1_318.MR.BECK-PAIGE_A0A1_INHABITION.0003.0001.2010.03.18.16.34.50.500000.21615932.IMA
> Block1.img
> reading from
> DB_A0A1_318.MR.BECK-PAIGE_A0A1_INHABITION.0003.0001.2010.03.18.16.34.50.500000.21615932.IMA...
> Getting Series No
> Scanning Directory
> INFO: Found 111 files in /Volumes/dubois/A0A1inhibition/DB_A0A1_318/Block1
> INFO: Scanning for Series Number 3
> INFO: found 107 files in series
> INFO: loading series header info.
>
> INFO: sorting.
> RunNo = 2
> INFO: (120 110 50), nframes = 107, ismosaic=1
> ERROR: incorreclty formatted version string syngo MR B17
> found in dicom tag 18,1020 (len = 3 != 6)
> Numaris Version: syngo MR B17 Maj = 0, Min=-1073775504, MinMin = 0
> mojo:/Volumes/dubois/A0A1inhibition/DB_A0A1_318/Block1 paige$ mri_convert
> -it dicom -ot analyze4d
> DB_A0A1_318.MR.BECK-PAIGE_A0A1_INHABITION.0003.0001.2010.03.18.16.34.50.500000.21615932.IMA
> Block1.img
> mri_convert -it dicom -ot analyze4d
> DB_A0A1_318.MR.BECK-PAIGE_A0A1_INHABITION.0003.0001.2010.03.18.16.34.50.500000.21615932.IMA
> Block1.img
> reading from
> DB_A0A1_318.MR.BECK-PAIGE_A0A1_INHABITION.0003.0001.2010.03.18.16.34.50.500000.21615932.IMA...
> Getting Series No
> Scanning Directory
> INFO: Found 111 files in /Volumes/dubois/A0A1inhibition/DB_A0A1_318/Block1
> INFO: Scanning for Series Number 3
> INFO: found 107 files in series
> INFO: loading series header info.
>
> INFO: sorting.
> RunNo = 2
> INFO: (120 110 50), nframes = 107, ismosaic=1
> ERROR: incorreclty formatted version string syngo MR B17
> found in dicom tag 18,1020 (len = 3 != 6)
> Numaris Version: syngo MR B17 Maj = -1073770984, Min=22021328, MinMin =
> -1610546680
> 107 DICOM 3.0 files in list
> Found 107 DICOM Files
> WARNING: NumberOfFrames 0 != Found Count of slices 107.
> reading DICOM image...
> -------------------------------------------------
> DICOM meta-header
>
> file name
> /Volumes/dubois/A0A1inhibition/DB_A0A1_318/Block1/DB_A0A1_318.MR.BECK-PAIGE_A0A1_INHABITION.0003.0001.2010.03.18.16.34.50.500000.21615932.IMA
> Date and time
> study date 20100318
> study time 160300.312000
> series time 162802.453000
> acquisition time 162802.453000
> Identification
> patient name DB_A0A1_318
> manufacturer SIEMENS
> Dimensions
> number of rows 880
> number of columns 960
> number of frames 107
> pixel width 2.13333
> pixel height 2.13333
> slice thickness 2.1
> field of view 1877.33
> image number 1 (might be not reliable)
> transfer syntax UID 1.2.840.10008.1.2.1
> Acquisition parameters
> echo time 25
> repetition time 3000
> inversion time not found
> echo number 1
> flip angle 1.5708
> bits allocated 16
> Spatial information
> first image position -1027.46 -12.1727 952.833
> last image position -1027.46 -12.1727 952.833
> image orientation 1 0 0 0 -0.00174528 -0.999998
> -------------------------------------------------
>
> TR=3000.00, TE=25.00, TI=0.00, flip angle=90.00
> i_ras = (-1, -0, 0)
> j_ras = (-0, 0.00174528, -0.999999)
> k_ras = (nan, nan, nan)
> Reslicing using trilinear interpolation
> MRIresample(): error inverting matrix; determinant is nan, matrix is:
> -2.133 -0.000 nan nan;
> -0.000 0.004 nan nan;
> 0.000 -2.133 nan nan;
> 0.000 0.000 0.000 1.000;
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