Hi,
I am very new to FMRI and would appreciate your help with my first attempt to use real data. I am trying to convert dicom images produced by a Siemens scanner to nii.gz format to be analysed by FSL FEAT. These BOLD images have 7 digit names without an extension and are in a folder on a CD which also contains a dicomdir file. Below you can see the command I have used and the output. The 001.nii.gz file has only one volume while the study consists of multiple volumes. Is there anything I should do differently.
Thanks,
Bahman
[root@localhost Desktop]# mri_convert -i temp/45516912 -ot nii 001.nii.gz mri_convert -i temp/45516912 -ot nii 001.nii.gz $Id: mri_convert.c,v 1.146.2.1 2007/11/30 23:18:44 greve Exp $ reading from temp/45516912... Getting Series No Scanning Directory INFO: Found 723 files in temp INFO: Scanning for Series Number 80 WARNING: searching dicom file temp/dicomdir for Manufacturer tag 0x8, 0x70 WARNING: the result could be a mess. WARNING: searching dicom file temp/dicomdir for Manufacturer tag 0x8, 0x70 WARNING: the result could be a mess. INFO: found 9 files in series INFO: loading series header info.
INFO: sorting. RunNo = 79 INFO: (128 128 9), nframes = 1, ismosaic=0 AutoAlign matrix detected AutoAlign Matrix --------------------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000;
FileName temp/45516912 Identification NumarisVer syngo MR 2004A 4VA25A ScannerModel Symphony PatientName **** Date and time StudyDate 20070216 StudyTime 110335.484000 SeriesTime 112105.578000 AcqTime 112059.464999 Acquisition parameters PulseSeq epfid2d1_64 Protocol BOLD 1 (Dec 4) PhEncDir ROW EchoNo 0 FlipAngle 90 EchoTime 40 InversionTime -1 RepetitionTime 2000 PhEncFOV 240 ReadoutFOV 240 Image information RunNo 79 SeriesNo 80 ImageNo 1 NImageRows 128 NImageCols 128 NFrames 1 SliceArraylSize 9 IsMosaic 0 ImgPos 117.6862 129.3817 45.4824 VolRes 1.8750 1.8750 10.0000 VolDim 128 128 9 Vc -1.0000 0.0010 -0.0086 Vr -0.0000 -0.9940 -0.1097 Vs -0.0087 -0.1097 0.9939 VolCenter -2.6996 5.2827 76.0057 TransferSyntaxUID 1.2.840.10008.1.2.1 INFO: no Siemens slice order reversal detected (good!). TR=2000.00, TE=40.00, TI=-1.00, flip angle=90.00 i_ras = (-0.999962, 0.000951853, -0.00862145) j_ras = (-2.16616e-10, -0.99396, -0.109738) k_ras = (-0.00867384, -0.109734, 0.993923) writing to 001.nii.gz...
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Not sure what's going on. Did you really collect 79 runs? Was there more than one time point in the 79th run? There is a button on the Siemens console that causes each time point of each series to be saved as separate series. If you checked this button, then you'll have to unpack each time point and then concatenate them together. And after that, you'll make sure that that button is not checked!
doug
HAMID REZA DABIRZADEH wrote:
Hi,
I am very new to FMRI and would appreciate your help with my first attempt to use real data. I am trying to convert dicom images produced by a Siemens scanner to nii.gz format to be analysed by FSL FEAT. These BOLD images have 7 digit names without an extension and are in a folder on a CD which also contains a dicomdir file. Below you can see the command I have used and the output. The 001.nii.gz file has only one volume while the study consists of multiple volumes. Is there anything I should do differently.
Thanks,
Bahman
[root@localhost Desktop]# mri_convert -i temp/45516912 -ot nii 001.nii.gz mri_convert -i temp/45516912 -ot nii 001.nii.gz $Id: mri_convert.c,v 1.146.2.1 2007/11/30 23:18:44 greve Exp $ reading from temp/45516912... Getting Series No Scanning Directory INFO: Found 723 files in temp INFO: Scanning for Series Number 80 WARNING: searching dicom file temp/dicomdir for Manufacturer tag 0x8, 0x70 WARNING: the result could be a mess. WARNING: searching dicom file temp/dicomdir for Manufacturer tag 0x8, 0x70 WARNING: the result could be a mess. INFO: found 9 files in series INFO: loading series header info.
INFO: sorting. RunNo = 79 INFO: (128 128 9), nframes = 1, ismosaic=0 AutoAlign matrix detected AutoAlign Matrix --------------------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000;
FileName temp/45516912 Identification NumarisVer syngo MR 2004A 4VA25A ScannerModel Symphony PatientName **** Date and time StudyDate 20070216 StudyTime 110335.484000 SeriesTime 112105.578000 AcqTime 112059.464999 Acquisition parameters PulseSeq epfid2d1_64 Protocol BOLD 1 (Dec 4) PhEncDir ROW EchoNo 0 FlipAngle 90 EchoTime 40 InversionTime -1 RepetitionTime 2000 PhEncFOV 240 ReadoutFOV 240 Image information RunNo 79 SeriesNo 80 ImageNo 1 NImageRows 128 NImageCols 128 NFrames 1 SliceArraylSize 9 IsMosaic 0 ImgPos 117.6862 129.3817 45.4824 VolRes 1.8750 1.8750 10.0000 VolDim 128 128 9 Vc -1.0000 0.0010 -0.0086 Vr -0.0000 -0.9940 -0.1097 Vs -0.0087 -0.1097 0.9939 VolCenter -2.6996 5.2827 76.0057 TransferSyntaxUID 1.2.840.10008.1.2.1 INFO: no Siemens slice order reversal detected (good!). TR=2000.00, TE=40.00, TI=-1.00, flip angle=90.00 i_ras = (-0.999962, 0.000951853, -0.00862145) j_ras = (-2.16616e-10, -0.99396, -0.109738) k_ras = (-0.00867384, -0.109734, 0.993923) writing to 001.nii.gz...
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Baham,
You can use mri_concat to combine all the frames into one file. That is, first use mri_convert as you have done to create the ###.nii.gz files for each frame, then:
mri_concat --i 001.nii.gz 002.nii.gz 003.nii.gz (etc..) \ --o session.nii.gz
will concatenate the frames into one file (session.nii.gz).
Nick
On Wed, 2008-01-02 at 00:40 -0500, HAMID REZA DABIRZADEH wrote:
Hi,
I am very new to FMRI and would appreciate your help with my first attempt to use real data. I am trying to convert dicom images produced by a Siemens scanner to nii.gz format to be analysed by FSL FEAT. These BOLD images have 7 digit names without an extension and are in a folder on a CD which also contains a dicomdir file. Below you can see the command I have used and the output. The 001.nii.gz file has only one volume while the study consists of multiple volumes. Is there anything I should do differently.
Thanks,
Bahman
[root@localhost Desktop]# mri_convert -i temp/45516912 -ot nii 001.nii.gz mri_convert -i temp/45516912 -ot nii 001.nii.gz $Id: mri_convert.c,v 1.146.2.1 2007/11/30 23:18:44 greve Exp $ reading from temp/45516912... Getting Series No Scanning Directory INFO: Found 723 files in temp INFO: Scanning for Series Number 80 WARNING: searching dicom file temp/dicomdir for Manufacturer tag 0x8, 0x70 WARNING: the result could be a mess. WARNING: searching dicom file temp/dicomdir for Manufacturer tag 0x8, 0x70 WARNING: the result could be a mess. INFO: found 9 files in series INFO: loading series header info.
INFO: sorting. RunNo = 79 INFO: (128 128 9), nframes = 1, ismosaic=0 AutoAlign matrix detected AutoAlign Matrix --------------------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000;
FileName temp/45516912 Identification NumarisVer syngo MR 2004A 4VA25A ScannerModel Symphony PatientName **** Date and time StudyDate 20070216 StudyTime 110335.484000 SeriesTime 112105.578000 AcqTime 112059.464999 Acquisition parameters PulseSeq epfid2d1_64 Protocol BOLD 1 (Dec 4) PhEncDir ROW EchoNo 0 FlipAngle 90 EchoTime 40 InversionTime -1 RepetitionTime 2000 PhEncFOV 240 ReadoutFOV 240 Image information RunNo 79 SeriesNo 80 ImageNo 1 NImageRows 128 NImageCols 128 NFrames 1 SliceArraylSize 9 IsMosaic 0 ImgPos 117.6862 129.3817 45.4824 VolRes 1.8750 1.8750 10.0000 VolDim 128 128 9 Vc -1.0000 0.0010 -0.0086 Vr -0.0000 -0.9940 -0.1097 Vs -0.0087 -0.1097 0.9939 VolCenter -2.6996 5.2827 76.0057 TransferSyntaxUID 1.2.840.10008.1.2.1 INFO: no Siemens slice order reversal detected (good!). TR=2000.00, TE=40.00, TI=-1.00, flip angle=90.00 i_ras = (-0.999962, 0.000951853, -0.00862145) j_ras = (-2.16616e-10, -0.99396, -0.109738) k_ras = (-0.00867384, -0.109734, 0.993923) writing to 001.nii.gz...
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freesurfer@nmr.mgh.harvard.edu
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Doug Greve -
HAMID REZA DABIRZADEH -
Nick Schmansky