Hi,
I'm new to fMR and am using mri_convert to convert from siemens dicom to
analyze/spm format.I ran the command below and had a couple of questions:
1 - Why does the first INFO: line say that 807 files were found when only 805
were input?
2 - Why were only 800 of 805 files converted?
3 - As it says at the end of the output, the axial plane is flipped. Is there
any way I can prevent this?
Thanks for your help,
Alex
mri_convert -it siemens_dicom 21851740 -ot spm ../test
mri_convert -it siemens_dicom 21851740 -ot spm ../test
reading from 21851740...
Getting Series No
Scanning Directory
INFO: Found 807 files in
/data/flanders/work/alex/freesurfer/subjects_pace/epi_test/04271947
INFO: Scanning for Series Number 2
INFO: found 800 files in series
INFO: loading series header info.
INFO: sorting.
RunNo = 1
INFO: ( 64 60 21), nframes = 800, ismosaic=1
Numaris Version: syngo MR 2004V 4VB11D Maj = 4, Min=1, MinMin = 1
Computing TR with number of slices
Repetition Time = 1420, TR = 29820 ms
FileName
/data/flanders/work/alex/freesurfer/subjects_pace/epi_test/04271947/21851800
Identification
NumarisVer syngo MR 2004V 4VB11D
ScannerModel Avanto
PatientName Fornito^Alex^^^Mr
Date and time
StudyDate 20060427
StudyTime 192350.703000
SeriesTime 192556.781000
AcqTime 192554.055005
Acquisition parameters
PulseSeq epfid2d1_60
Protocol ep2d_800
PhEncDir COL
EchoNo 0
FlipAngle 78
EchoTime 26
InversionTime 26
RepetitionTime 1420
PhEncFOV 206.25
ReadoutFOV 220
Image information
RunNo 1
SeriesNo 2
ImageNo 1
NImageRows 300
NImageCols 320
NFrames 800
SliceArraylSize 21
IsMosaic 1
ImgPos 106.2426 139.4769 -20.2630
VolRes 3.4375 3.4375 5.0000
VolDim 64 60 21
Vc -0.9981 -0.0053 0.0606
Vr 0.0000 -0.9962 -0.0873
Vs 0.0608 -0.0872 0.9943
VolCenter -0.3610 31.5859 29.5993
TransferSyntaxUID 1.2.840.10008.1.2.1
should never get here
INFO: no Siemens slice order reversal detected (good!).
TR=29820.00, TE=26.00, TI=26.00, flip angle=78.00
i_ras = (-0.998149, -0.00531035, 0.0605839)
j_ras = (3.3967e-08, -0.996181, -0.0873174)
k_ras = (0.0608162, -0.0871557, 0.994337)
writing to ../test...
Analyze Output Matrix
-3.431 0.000 0.304 109.370;
-0.018 -3.424 -0.436 143.355;
0.208 -0.300 4.972 -25.143;
0.000 0.000 0.000 1.000;
--------------------
INFO: set hdr.hist.orient to 'transverse flipped'
INFO: set hdr.hist.orient to 'transverse flipped'
INFO: set hdr.hist.orient to 'transverse flipped'
INFO: set hdr.hist.orient to 'transverse flipped'
INFO: set hdr.hist.orient to 'transverse flipped'
INFO: set hdr.hist.orient to 'transverse flipped'
INFO: set hdr.hist.orient to 'transverse flipped'
INFO: set hdr.hist.orient to 'transverse flipped'
INFO: set hdr.hist.orient to 'transverse flipped'
INFO: set hdr.hist.orient to 'transverse flipped'
...
Alex Fornito
M.Psych/PhD (clin. neuro.) candidate
Melbourne Neuropsychiatry Centre and Department of Psychology
National Neuroscience Facility
The University of Melbourne
Levels 2 & 3, Alan Gilbert Building
161 Barry St
Carlton South Vic 3053 Australia
Ph: +61 3 8344 1624
Fax: +61 3 9348 0469
email: [EMAIL PROTECTED]
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
