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
--
Kevin Teich
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