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
[EMAIL PROTECTED] 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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