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
>
> [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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