/space/orsay/2/knutsen the auto intensity normalization works ok...but yeah i can't seem to transfer the register.dat from one volume with same parameters as the rest of the functionals, to the bold sub-dir and then paint my activation maps using that register.dat without getting a segmentation fault.
On Tue, 26 Jul 2005, Kevin Teich wrote: > > Tamara, are you still having a problem with this? If so, can you send me > your SUBJECTS_DIR? > > > On Fri, 22 Jul 2005, Doug Greve wrote: > > > > > For the over-saturation, you can adjust the brightness with the fmov > > entry box. You can also click in the image window and hit 'i' to > > toggle the automatic intensity normalization. We'll have to wait until > > I'm back in the office next week to look at the tksurfer problem -- > > unless Kevin can look at it sooner ... > > > > doug > > > > On Fri, 22 Jul 2005, Tamara Knutsen wrote: > > > >> for data acquired using the multiecho sequence and undistorting it using > >> anders' program, i get oversaturated images in the tkregister program, > >> making it impossible to register to the anatomical. however i took other > >> in-session functionals that i can use to register successfully. but if i > >> copy these register.dat files into the bold directory and try to use them > >> to paint the activation maps onto the anatomical surfaces, and then try to > >> view the surfaces, i get a segmentation fault. > >> > >> for instance, in /space/annecy/19/users/knutsen/050126Edgar > >> i created the register.dat using the MErecon/005 > >> and copied this into the bold directory. then ran the paint.csh and > >> surf-lh.csh scripts in the scripts directory and got this segmentation > >> fault: > >> > >> [whatever:scripts] (nmr-dev-env) csh -f paint.csh > >> cat: /usr/local/freesurfer/dev/fsfast/docs/version: No such file or > >> directory > >> ----------------------------------------------------------------- > >> paint-sess logfile is > >> /autofs/space/annecy_019/users/knutsen/050126Edgar/mystudy/log/paint-sess.log > >> ----------------------------------------------------------------- > >> INFO: painting onto white > >> grep: /autofs/space/annecy_019/users/knutsen/050126Edgar/session.info: No > >> such file or directory > >> SpaceDir is > >> SpaceSubDir is > >> INFO: setting srcsubject to > >> Fri Jul 22 11:04:56 EDT 2005 > >> SpaceDir is > >> INFO: Painting onto edgar2 > >> Using Float2Int = round > >> ---------------------------------------- > >> /autofs/space/annecy_019/users/knutsen/050126Edgar/mystudy > >> mri_vol2surf --srcvol > >> /autofs/space/annecy_019/users/knutsen/050126Edgar/bold/PPA//pl_fa/sig > >> --src_type bfloat --srcreg > >> /autofs/space/annecy_019/users/knutsen/050126Edgar/bold/register.dat > >> --surf white --hemi lh --projfrac 0 --frame 0 --out_type paint --float2int > >> round --mapmethod nnf --o > >> /autofs/space/annecy_019/users/knutsen/050126Edgar/bold/PPA//pl_fa/sig-0-lh.w > >> --nvox > >> /autofs/space/annecy_019/users/knutsen/050126Edgar/bold/PPA//pl_fa/white-lh.nvox > >> ---------------------------------------- > >> INFO: output format is paint > >> srcvol = > >> /autofs/space/annecy_019/users/knutsen/050126Edgar/bold/PPA//pl_fa/sig > >> srctype = bfloat > >> srcreg = > >> /autofs/space/annecy_019/users/knutsen/050126Edgar/bold/register.dat > >> srcregold = 0 > >> srcwarp unspecified > >> surf = white > >> hemi = lh > >> interp = nearest > >> float2int = round > >> INFO: float2int code = 0 > >> INFO: bvolumeRead: min = -8.91759, max = 14.6838 > >> Done loading volume > >> Reading surface /space/orsay/2/knutsen//edgar2/surf/lh.white > >> Done reading source surface > >> Mapping Source Volume onto Source Subject Surface > >> vol2surf_linear: nhits = 76996/150625 > >> Done mapping volume to surface > >> Number of source voxels hit = 4931 > >> avg = 0.410, stdev = 1.414, min = -6.978, max = 10.800 > >> Fri Jul 22 11:05:00 EDT 2005 > >> SpaceDir is > >> INFO: Painting onto edgar2 > >> Using Float2Int = round > >> ---------------------------------------- > >> /autofs/space/annecy_019/users/knutsen/050126Edgar/mystudy > >> mri_vol2surf --srcvol > >> /autofs/space/annecy_019/users/knutsen/050126Edgar/bold/PPA//pl_fa/sig > >> --src_type bfloat --srcreg > >> /autofs/space/annecy_019/users/knutsen/050126Edgar/bold/register.dat > >> --surf white --hemi rh --projfrac 0 --frame 0 --out_type paint --float2int > >> round --mapmethod nnf --o > >> /autofs/space/annecy_019/users/knutsen/050126Edgar/bold/PPA//pl_fa/sig-0-rh.w > >> --nvox > >> /autofs/space/annecy_019/users/knutsen/050126Edgar/bold/PPA//pl_fa/white-rh.nvox > >> ---------------------------------------- > >> INFO: output format is paint > >> srcvol = > >> /autofs/space/annecy_019/users/knutsen/050126Edgar/bold/PPA//pl_fa/sig > >> srctype = bfloat > >> srcreg = > >> /autofs/space/annecy_019/users/knutsen/050126Edgar/bold/register.dat > >> srcregold = 0 > >> srcwarp unspecified > >> surf = white > >> hemi = rh > >> interp = nearest > >> float2int = round > >> INFO: float2int code = 0 > >> INFO: bvolumeRead: min = -8.91759, max = 14.6838 > >> Done loading volume > >> Reading surface /space/orsay/2/knutsen//edgar2/surf/rh.white > >> Done reading source surface > >> Mapping Source Volume onto Source Subject Surface > >> vol2surf_linear: nhits = 72327/148729 > >> Done mapping volume to surface > >> Number of source voxels hit = 4443 > >> avg = 0.391, stdev = 1.336, min = -6.783, max = 9.580 > >> ---------------------------------------------------------- > >> Fri Jul 22 11:05:03 EDT 2005 > >> > >> paint-sess completed SUCCESSFULLY > >> > >> [whatever:scripts] (nmr-dev-env) csh -f surf-lh.csh > >> cat: /usr/local/freesurfer/dev/fsfast/docs/version: No such file or > >> directory > >> grep: /autofs/space/annecy_019/users/knutsen/050126Edgar/session.info: No > >> such file or directory > >> ----------------------------------------------------------------- > >> surf-sess logfile is > >> /autofs/space/annecy_019/users/knutsen/050126Edgar/mystudy/log/surf-sess.PPA.pl_fa.log > >> ----------------------------------------------------------------- > >> ------------------------------------------------------ > >> ------------------------------------------------------ > >> Session: 050126Edgar ---- > >> ------ lh hemisphere ------ > >> grep: /autofs/space/annecy_019/users/knutsen/050126Edgar/session.info: No > >> such file or directory > >> wfile is > >> /autofs/space/annecy_019/users/knutsen/050126Edgar/bold/PPA//pl_fa/sig-0-lh.w > >> ------------ tcl file ----------- > >> set val > >> /autofs/space/annecy_019/users/knutsen/050126Edgar/bold/PPA//pl_fa/sig-0-lh.w > >> sclv_read_binary_values 0 > >> set curv lh.curv > >> read_binary_curv; > >> set curvflag 1; > >> source /usr/local/freesurfer/dev/lib/tcl/readenv.tcl > >> open_window > >> rotate_brain_y 90 > >> sclv_set_current_field 0 > >> redraw > >> --------------------------------- > >> ---------------------------------------------------------- > >> /autofs/space/annecy_019/users/knutsen/050126Edgar/bold/PPA/pl_fa > >> tksurfer -edgar2 lh inflated -tcl /tmp/surf-sess-18404.tcl > >> ---------------------------------------------------------- > >> Segmentation fault > >> Fri Jul 22 11:05:10 EDT 2005 > >> > >> > >> > >> > >> > > > > > > -- Tamara Knutsen http://www.nmr.mgh.harvard.edu/~knutsen _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
