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