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: alexander.fornito@wh.org.au
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug, Thanks for your speedy response. The image comes up fine in SPM, but not in other programs like MRIcro or FSLview, where the anterior of the image in the axial plane faces down instead of up. Is there any (relatively) straightforward I can adjust this through mri_convert? Thanks again, Alex
-----Original Message----- From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Wed 10/4/2006 2:03 PM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Converting DICOMs
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Doug Greve -
Fornito, Alexander