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