is there an error? It looks like it converted fine. The signal intensities are essentially arbitrary until the intensity normalization. The volume looks okay (the lines in it are from reslicing it into standard RAS coordinates). Did you process it further?
cheers, Bruce
On Thu, 23 Mar 2006 ingeam@student.sv.uio.no wrote:
Hi, I'm a new Freesurfer user, currently working with Fjell and Walhovd in Oslo.
When trying to convert some new scans with mri_convert there seems to be a problem with the reconstruction, also the signal intensity is in the 300-500 range. See attached image. It does not return any errors.
Could someone please point me in the right direction here?
Thank you Inge K Amlien
Running on: Freesurfer centos4 x86_64 stable 3.0 Fedore Core4
Output from mri_convert: mri_convert /labdata/lab-data/testinge/E0000002/1.3.12.2.1107.5.2.6.22226.30000005112107174770300000649/E0000002_2_002.dcm /labdata/lab-data/testinge/testE0000002/mri/orig/001.mgz reading from /labdata/lab-data/testinge/E0000002/1.3.12.2.1107.5.2.6.22226.30000005112107174770300000649/E0000002_2_002.dcm... Getting Series No INFO: Found 130 files in /labdata/lab-data/testinge/E0000002/1.3.12.2.1107.5.2.6.22226.30000005112107174770300000649 INFO: Scanning for Series Number 2 Scanning Directory INFO: found 128 files in series INFO: loading series header info. INFO: slice direction constructed from image direction cosines.
INFO: sorting. RunNo = 1 INFO: Handedness changed to left-handed. INFO: (512 512 128), nframes = 1, ismosaic=0 FileName /labdata/lab-data/testinge/E0000002/1.3.12.2.1107.5.2.6.22226.30000005112107174770300000649/E0000002_2_716.dcm Identification NumarisVer syngo MR 2004A 4VA25A ScannerModel Symphony PatientName E0000002 Date and time StudyDate 20051121 StudyTime 094537.984000 SeriesTime 095542.281000 AcqTime 094657.180012 Acquisition parameters PulseSeq *tfl3d1 Protocol t1_3d_mpr_sag PhEncDir ROW EchoNo 0 FlipAngle 15 EchoTime 3.19 InversionTime 1100 RepetitionTime 2730 PhEncFOV 0 ReadoutFOV 0 Image information RunNo 1 SeriesNo 2 ImageNo 128 NImageRows 512 NImageCols 512 NFrames 1 SliceArraylSize 0 IsMosaic 0 ImgPos -91.5886 131.5105 125.9759 VolRes 0.5000 0.5000 1.3300 VolDim 512 512 128 Vc 0.0297 -0.9996 0.0000 Vr -0.0000 -0.0000 -1.0000 Vs -0.9996 -0.0297 0.0000 VolCenter -172.8739 1.0416 -2.0241 TransferSyntaxUID 1.2.840.10008.1.2.1 INFO: no Siemens slice order reversal detected (good!). TR=2730.00, TE=3.19, TI=1100.00, flip angle=15.00 i_ras = (0.0296663, -0.99956, 0) j_ras = (-0, -0, -1) k_ras = (-0.99956, -0.0296663, 0) writing to /labdata/lab-data/testinge/testE0000002/mri/orig/001.mgz...
Scan info from nICE: Manufacure's model name (0008,1090): Symphony
Scanning sequenece (0018,0020): IR\GR
Scanning variant (0018,0021): SP\MP
Scan options (0018,0022): IR
Acquisition type (0018,0023): 3D
Scan (Sequence) Name (0018,0024): *tfl3d1
Protocol Name (0018,1030): t1_3d_mpr_sag
Repetition time, TR (ms)(0018,0080): 2730.0
Echo time, TE (ms) (0018,0081): 3.2
Inversion time, TI (ms) (0018,0082): 1100.000
Flip angle (deg) (0018,1314): 15
Pixel spacing X (mm) (0028,0030): 0.5000
Pixel spacing Y (mm) (0028,0030): 0.5000
Slice thickness (mm) (0018,0050): 1.3300
Slice spacing or gap (mm) (0018,0088): 0.0000
FoV (freq*phase, mm): 256.0000 * 256.0000
Rect. FoV percentage: 100.0
No of PE steps (0018,0089): 192
Turbo Factor (ETL) (0018,0091): 1
Scan Percentage (0018,0093): 75.0
Pixel Bandwidth (Hz) (0018,0095): 190.0
Number of averages (0018,0083): 1
Recon resolution (Rows) (0028,0010): 512
Recon resolution (Columns) (0028,0011): 512
Image matrix size (X * Y pixels): 512 * 512
Scan number (0020,0012): 1
Image (instance) number (0020,0013): 128
Series number (0020,0011): 2