[Freesurfer] mkbrainmask-sess
Hi All, just a quick note to let you know that 3.0.2's (centos4 x86_64) mkbrainmask-sess does not really parse the -run nth parameter it specifies in its help text. Haven't found time to implement a fix yet, but it is a minor issue anyway... Ahoi Sebastian -- Sebastian Moeller Tel.: 04 21 - 2 18 - 78 38 oder 96 91 Fax.: 04 21 - 2 18 - 90 04 GSM: 01 62 - 3 25 45 59 [EMAIL PROTECTED] AG Kreiter / FB 2 Institut fuer Hirnforschung III Abteilung Theoretische Neurobiologie Universitaet Bremen Biogarten Hochschulring 16a Postfach 33 04 40 28359 Bremen ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Bad scans/normalization
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? 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. FoV (freq*phase, mm): 256. * 256. 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
Re: [Freesurfer] Bad scans/normalization
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. FoV (freq*phase, mm): 256. * 256. 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
Re: [Freesurfer] Bad scans/normalization
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. FoV (freq*phase, mm): 256. * 256. 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
