Hi Bruce, I tried everything again and again, and the area file is created after orig. But still the command mris_convert produces the error:
mris_convert -c area /li2/freesurfer/freesurfer_alpha/subjects/t1xxl/surf/rh.orig /li2/freesurfer/freesurfer_alpha/subjects/t1xxl/surf/rh.area.asc MRISreadBinaryCurvature: incompatible vertex number in file /li2/freesurfer/freesurfer_alpha/subjects/t1xxl/surf/rh.area Is the "-c area" correct? Might the mris_convert be too old, too? (It is from Feb 1 2001). Thanks, Frederick --- Bruce Fischl <[EMAIL PROTECTED]> wrote: > Hi Frederick, > > I'm not sure what's wrong, as this works fine for > me. Check the dates on > your files, and make sure that the area file was > created after the orig. If > you are still having problems and can put your data > somewhere we can look > at it, we will. > > cheers, > Bruce > > -------------------------------------------------------- > Bruce Fischl email: > [EMAIL PROTECTED] > Mass. General Hosp. NMR Center. > tel:(617)-726-4897 > Rm. 2328, Building 149, 13th Street > fax:(617)-726-7422 > Charlestown, MA 02129 USA > > > > > On Tue, 14 May 2002, Frederick Klauschen wrote: > > > Hi Bruce, > > > > I downloaded the updated > > mris_smooth.Linux > > from the path you indicated below and I moved the > file > > to /freesurfer_alpha/bin/Linux/mris_smooth. > > Then I restartet the CREATE_SURFACE process and > got > > a new ?h.area file. > > Then I transformed to ascii again: > > > > mris_convert -c area > > /freesurfer_alpha/subjects/t1normal/surf/lh.orig > > > /freesurfer_alpha/subjects/t1normal/surf/lh.area.asc > > MRISreadBinaryCurvature: incompatible vertex > number in > > file > > /li2/freesurfer/freesurfer_alpha/subjects/t1normal > > /surf/lh.area > > > > A new lh.area.asc is output, the vertex number is > the > > same as before but the area values are all zero! > > > > Thanks, > > Frederick > > > > > > > > --- Bruce Fischl <[EMAIL PROTECTED]> > wrote: > > > Hi Frederick, > > > > > > the thickness and area measures should be in mm > and > > > mm^2 respectively. I > > > think you have an old version of mris_smooth > that > > > generates incorrect > > > ?h.area files, which is why you are getting > > > alternate zeros. I've put new > > > versions on our ftp site: > > > > > > ftp surfer.nmr.mgh.harvard.edu > > > Connected to surfer.nmr.mgh.harvard.edu. > > > 220 surfer.nmr.mgh.harvard.edu FTP server > (Version > > > wu-2.6.1-16.7x.1) ready. > > > Name (surfer.nmr.mgh.harvard.edu:fischl): > anonymous > > > 331 Guest login ok, send your complete e-mail > > > address as password. > > > Password: > > > 230-The response 'fischl@nmr' is not valid > > > 230-Next time please use your e-mail address as > your > > > password > > > 230- for example: > > > [EMAIL PROTECTED] > > > 230 Guest login ok, access restrictions apply. > > > Remote system type is UNIX. > > > Using binary mode to transfer files. > > > ftp> cd /space/outgoing/fsdev > > > 250 CWD command successful. > > > ftp> ls mris_smooth* > > > 227 Entering Passive Mode > (132,183,202,158,9,149) > > > 150 Opening ASCII mode data connection for > directory > > > listing. > > > -rwxrwxr-x 1 5499 160 1639184 May 13 > > > 16:12 mris_smooth.IRIX > > > -rwxrwxr-x 1 5499 160 2546764 May 13 > > > 16:12 mris_smooth.Linux > > > -rwxrwxr-x 1 5499 160 2378232 May 13 > > > 16:12 mris_smooth.Solaris > > > > > > > > > cheers, > > > Bruce > > > > > > > > > -------------------------------------------------------- > > > Bruce Fischl email: > > > [EMAIL PROTECTED] > > > Mass. General Hosp. NMR Center. > > > tel:(617)-726-4897 > > > Rm. 2328, Building 149, 13th Street > > > fax:(617)-726-7422 > > > Charlestown, MA 02129 USA > > > > > > > > > On Sun, 12 May 2002, Frederick Klauschen wrote: > > > > > > > Hi, > > > > > > > > I have done the conversion of the ?h.thickness > and > > > > ?h.area files to ascii format. > > > > I have got an array of the size 163993x5. Each > row > > > > contains an index, three coordinates and > another > > > > value, which probably is the thickness/area. > > > > Unfortunately, I was not able to find any > details > > > > about this thickness/area value (unit?). > > > > In order to calculate the grey matter volume, > > > > do I just have to sum up the thickness or > > > > rather take the average thickness and weigh > with > > > > the total area(why is only every second entry > in > > > the > > > > area field (5th column) of ?h.area.asc > different > > > from > > > > zero?)? > > > > > > > > Thanks for any help, > > > > Frederick > > > > > > > > > > > > > > > > > __________________________________________________ > > > > Do You Yahoo!? > > > > LAUNCH - Your Yahoo! Music Experience > > > > http://launch.yahoo.com > > > > > > > > > > > __________________________________________________ > > Do You Yahoo!? > > LAUNCH - Your Yahoo! Music Experience > > http://launch.yahoo.com > > > __________________________________________________ Do You Yahoo!? LAUNCH - Your Yahoo! Music Experience http://launch.yahoo.com
