On Wed, 4 Oct 2006, Fornito, Alexander wrote:
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?
That's just the number of files in the directory (includes "." and "..", which is where the extra 2 come from)
2 - Why were only 800 of 805 files converted?
Of the 805 files, 800 of them belonged to the series you were converting. The other files were either non-dicom or dicoms but not in your series (eg, a localizer).
3 - As it says at the end of the output, the axial plane is flipped. Is there any way I can prevent this?
The axial plane is not actually flipped. The msg:
INFO: set hdr.hist.orient to 'transverse flipped'
means that a flag in the header is set to 'transverse flipped'. I don't know what software packages actually use this info. SPM will/should read the .mat file created instead of the orient field in the hdr.
doug
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: alexander.fornito@wh.org.au
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