Hello fellow Freesurfers!
We are at the startup of a new project, and we have some concerns about the quality of our scans. There seems to be white/grey contrast problems. In the original scan (001_mgz.png) and T1 the contrasts are quite clear, but in brainmask the contrasts are almost completely gone, mainly in the superior region. We are concerned this might lead to underestimated cortical thickness, and probably a bunch of other problems as well.
Can somebody tell me if there is a problem with our scans, so we can change this while still at the start of the project? Are there any freesurfer commands I should try, maybe options for normalize?
Regards Inge Amlien University of Oslo
___________________ Freesurfer 3.01
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
