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;
_______________________________________________
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.
