ok. it seems to be an osx problem. using a more recent version on a mac did not work, but the orientations were fine when i ran it on a linux box. i can just use that machine to do the motion correction for all of these subjects.
thanks for your help! -cate > Yes, the problem is with the matfile. This is rather strange since we generate > the matfile. It might be some interaction with osx. Do you have a linux box > your can try it out on? This also looks like it might be a fairly old version, > can you download a more recent version and see if it works on osx? > > doug > > > > > > Catherine Hartley wrote: >> Hi, >> >> I'm still having problems with the rawavg.mgz volume being generated with >> incorrect orientations. I gave Jenni two 00?.mgz volumes and she was able >> to generate a correctly-oriented rawavg. Our two log files look very >> different, but I'm not able to figure out the problem by looking at them. >> To start with, the i_ras, j_ras, and k_ras value for the 00?.mgz volumes are >> different in each of our log files. Mine also has several warnings in which >> it says that it cannot read a matfile, and that the hist.orient value is not >> valid. I've attached the log files. Any suggestions would be very very >> welcome. >> >> Thanks in advance, >> Cate >> >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
