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