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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