Re: [Freesurfer] wmfill

[Bruce Fischl]

yes, that is incorrect. If there is no talalairach you need to enter the 
"volume scanner" coords from tkmedit (you can turn them on under 
view->information).

cheers,
Bruce
On Mon, 6 Dec 2004, Margaret Duff wrote:
in the manual it says if the talairach coordinates are not available,
enter the x,y,z locations from the volume index in the cursor area.  is
this not true anymore?  thanks, margaret
On Mon, 6 Dec 2004, Bruce Fischl
wrote:
Hi Margaret,
the points need to be specified in talairach coords  - it looks like you
are using voxels coords.
Bruce
On Mon, 6 Dec 2004, Margaret Duff wrote:
Hi,  I tried to manually set the cutting planes, but I was unable to get
the create surface to run.  My subjects info is at
/space/troy/1/users/FREESURFER/SM2S4_freesurfer and I tried to specify
coordinates (121 90 139) for the CC and (131 159 118) for the pons.  I
used the manuals troubleshooting to guide me, but is still cannot find
them.  The logfile I got is below.  Could something besides
specifying these coordinates be going wrong?  Thanks, Margaret
/space/lyon/1/home/inverse/freesurfer_alpha/bin/Linux/mri_fill -lval 255
-rval 80   -P 131 159 118  -C 121 90 139 -ccmask -T 1 -L
/space/troy/1/users/FREESURFER/SM2S4_freesurfer/mri/tmp/ponscall.dat
/space/troy/1/users/FREESURFER/SM2S4_freesurfer/mri/wm
/space/troy/1/users/FREESURFER/SM2S4_freesurfer/mri/filled
using 255 as fill val for left hemisphere.
using 80 as fill val for right hemisphere.
using Talairach position (131, 159, 118) as pons seed point
using Talairach position (121, 90, 139) as corpus callosum seed point
not using corpus callosum to mask possible location of pons.
logging cutting plane coordinates to
/space/troy/1/users/FREESURFER/SM2S4_freesurfer/mri/tmp/ponscall.dat...
voxel to talairach voxel transform
1.000   0.000   0.000   0.000;
0.000   1.000   0.000   0.000;
0.000   0.000   1.000   0.000;
0.000   0.000   0.000   1.000;
The seed point (121.00, 90.00, 139.00) is mapped to a voxel (15.27, -0.82.
166.72).
Make sure that the seed point is given in talaraich position or use -CV
option
INFO: volume does not have linear_transform set nor lta is given by
option.-xform.
INFO: use identity matrix as the talairach transform.
INFO: use src volume parameters for the talairach volume.
INFO: Modifying dst c_(r,a,s), using the transform dst
Using the seed to calculate the cutting plane
Verify whether the seed point is inside the volume first
Command Finished

On Wed, 1 Dec 2004,
Bruce Fischl wrote:
Hi Margaret,
if no talairach.xfm exists, then the fill may still find the cc and pons,
but it might not. You can always specify them manually be finding a
sagittal slice in which the cc is disconnected and a horizontal slice above
the cerebellar peduncles where the pons is disconnected.
cheers,
Bruce
On Wed, 1 Dec
2004, Margaret Duff wrote:
The log file is below.  And at the end it says command finished, not that
something went wrong.  I am not sure about the cutting planes or how to
specify them manually.  Thanks for your help.  Margaret
/space/lyon/1/home/inverse/freesurfer_alpha/bin/Linux/mri_fill -lval 255
-rval 80  -ccmask -T 1 -L
/space/troy/1/users/FREESURFER/SM2S4_freesurfer/mri/tmp/ponscall.dat
/space/troy/1/users/FREESURFER/SM2S4_freesurfer/mri/wm
/space/troy/1/users/FREESURFER/SM2S4_freesurfer/mri/filled
using 255 as fill val for left hemisphere.
using 80 as fill val for right hemisphere.
not using corpus callosum to mask possible location of pons.
logging cutting plane coordinates to
/space/troy/1/users/FREESURFER/SM2S4_freesurfer/mri/tmp/ponscall.dat...
voxel to talairach voxel transform
1.000   0.000   0.000   0.000;
0.000   1.000   0.000   0.000;
0.000   0.000   1.000   0.000;
0.000   0.000   0.000   1.000;
updating initial cc seed to Tal vol (121.00, 151.00, 77.00) TAL (15.27,
0.28, -12.82)
Looking for area (min, max) = (350, 1400)
area[0] = 365 (min = 350, max = 1400), aspect = 1.27 (min = 0.10, max =
0.75)
need search nearby
using +/- offset search region where offset is 3.....
using +/- offset search region where offset is 6.....
using +/- offset search region where offset is 9.....
using +/- offset search region where offset is 12.....
using +/- offset search region where offset is 15.....
using +/- offset search region where offset is 18.....
using +/- offset search region where offset is 21.....
area[0] = 1210 (min = 350, max = 1400), aspect = 0.37 (min = 0.10, max =
0.75)
corpus callosum seed point found at Tal vol: (121, 125, 162) TAL: (15.27,
85.28, 13.18)
min_slice = -1, min_area = 65536
Looking for area (min, max) = (350, 1400)
area[0] = 5435 (min = 350, max = 1400), aspect = 0.50 (min = 0.10, max =
0.75)
need search nearby
using +/- offset search region where offset is 3.....
using +/- offset search region where offset is 6.....
using +/- offset search region where offset is 9.....
area[0] = 488 (min = 350, max = 1400), aspect = 0.26 (min = 0.10, max =
0.75)
corpus callosum seed point found at Tal vol: (127, 97, 124) TAL: (9.27,
47.28, 41.18)
min_slice = -1, min_area = 65536
/space/lyon/1/home/inverse/freesurfer_alpha/bin/Linux/mri_fill: could not
find corpus callosum
No such file or directory
INFO: volume does not have linear_transform set nor lta is given by
option.-xform.
INFO: use identity matrix as the talairach transform.
INFO: use src volume parameters for the talairach volume.
INFO: Modifying dst c_(r,a,s), using the transform dst
Command Finished
On Tue, 30 Nov 2004, Bruce Fischl wrote:
Hi Margaret,
we need more information than that. Can you send us log files from trying
to run mri_fill? Is it finding the cutting planes? Have you tried
specifying them manually?
cheers,
Bruce
On Tue, 30 Nov 2004, Margaret Duff wrote:
Hi,  I keep getting an error message after I run Create Surface.  It is
similar to questions found in the archive but those solutions did not work
and this problem did not occur for the first 2 brains I reconstructed.  I
get an alert that the Images (filled): /subjectsdir/mri/filled/COR-001 not
found.  wmfill first.  I thought the first step was to fill the wm so
these files should have already been created.  Thanks for any help,
Margaret
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