Hi Bruce, Anders or Kristine will get back to you with those details, as my only experience with the actual scanner is lying in one.
The attached images were from one of the first scans, I will process some later ones to see if they turn out any better. Regards Inge Amlien University of Oslo, Norway >p.s. what coil are you using? There's a lot of dropoff towards the top of >the head, which may mean you are landmarking too low. Where do you >landmark before putting the subject in? > Hi Inge, > > you can look at Andre van der Kouwe's website: > > http://www.nmr.mgh.harvard.edu/~andre/ > > for some recommended protocols. His flip angle is quite a bit smaller than > yours (7 deg). The surfaces look reasonable although the data does seem > blurry. Is this true on all the subjects? Is this just one that moved a > lot? If you turn the brightness down you'll also see better g/w > distinction. > > cheers, > Bruce > > > On Wed, 14 Jun 2006, Inge K. > Amlien wrote: > >> 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 > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
