Hi Vasanth,
your orig.mgz hasn't been conformed. That is, it should be 1mm isotropic
in a 256^3 volume, but it's not:
mri_info /autofs/space/boba_001/users/nrecon/ARSS70_nrecon/mri/orig.mgz
Volume information for
/autofs/space/boba_001/users/nrecon/ARSS70_nrecon/mri/orig.mgz
type: MGH
dimensions: 256 x 256 x 128
voxel sizes: 1.0000, 1.0000, 1.3300
type: FLOAT (3)
fov: 256.000
xstart: -128.0, xend: 128.0
ystart: -128.0, yend: 128.0
zstart: -85.1, zend: 85.1
.
.
.
how did you generate it?
Bruce
On
Fri, 24 Mar 2006, Vasanth Pappu wrote:
Hi,
I am using recon-all and the norm.mgz's so far are only about half the brain.
I checked the input volumes and looked though the output to std and
everything seemed fine, so I am not sure what to do:
on machine vader
source /usr/local/freesurfer/nmr-std-env
setenv SUBJECTS_DIR /autofs/space/boba_001/users/nrecon/
which mri_ca_normalize
/usr/local/freesurfer/stable/bin//mri_ca_normalize
cd /autofs/space/boba_001/users/nrecon/ARSS70_nrecon/mri
mri_ca_normalize -mask brainmask.mgz nu.mgz
/usr/local/freesurfer/stable/average/RB_all_2006-02-15.gca
transforms/talairach.lta norm.mgz
output:
using MR volume brainmask.mgz to mask input volume...
reading 1 input volumes
reading atlas from
'/usr/local/freesurfer/stable/average/RB_all_2006-02-15.gca'...
setting gca type = Normal gca type
reading transform from 'transforms/talairach.lta'...
reading input volume from nu.mgz...
Note: program considers input volume #1 as the most T1-like
using real data threshold=56.0
using (109, 110, 82) as brain centroid...
mean wm in atlas = 109, using box (94,96,73) --> (123, 124,90) to find MRI wm
before smoothing, mri peak at 484
after smoothing, mri peak at 484, scaling input intensities by 0.225
scaling channel 0 by 0.224939
using 242283 sample points...
INFO: compute sample coordinates transform
1.724 -0.639 -2.451 142.880;
0.122 1.661 -0.265 -85.128;
2.012 0.112 1.598 -322.680;
0.000 0.000 0.000 1.000;
INFO: transform used
finding control points in Left_Cerebral_White_Matter....
found 38929 control points for structure...
bounding box (121, 85, 50) --> (177, 152, 94)
Left_Cerebral_White_Matter: limiting intensities to 92.0 --> 111.0
87 of 225 (38.7%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 38531 control points for structure...
bounding box (116, 86, 62) --> (172, 156, 102)
Right_Cerebral_White_Matter: limiting intensities to 95.0 --> 108.0
90 of 179 (50.3%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3087 control points for structure...
bounding box (132, 135, 50) --> (150, 158, 68)
Left_Cerebellum_White_Matter: limiting intensities to 82.0 --> 96.0
18 of 52 (34.6%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2900 control points for structure...
bounding box (123, 136, 61) --> (144, 161, 76)
Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 102.0
23 of 58 (39.7%) samples deleted
finding control points in Brain_Stem....
found 3414 control points for structure...
bounding box (138, 130, 62) --> (152, 170, 78)
Brain_Stem: limiting intensities to 89.0 --> 97.0
37 of 66 (56.1%) samples deleted
using 580 total control points for intensity normalization...
bias field = 1.037 +- 0.088
0 of 219 control points discarded
writing normalized volume to norm.mgz...
freeing GCA...done.
normalization took 1 minutes and 29 seconds.
But when I look at norm.mgz, the whole brain is not shown:
tkmedit -f /autofs/space/boba_001/users/nrecon/ARSS70_nrecon/mri/norm.mgz
I checked the inputs brainmask.mgz and nu.mgz, and they seem ok:
tkmedit -f
/autofs/space/boba_001/users/nrecon/ARSS70_nrecon/mri/brainmask.mgz
tkmedit -f /autofs/space/boba_001/users/nrecon/ARSS70_nrecon/mri/nu.mgz
how do I check if the transforms/talairach.lta is ok?
Thanks,
Vasanth
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