Hi Falk,
I just tried it and it seemed to work for me:
mri_info Gaab20070225a/mri/rawavg.mgz
Volume information for Gaab20070225a/mri/rawavg.mgz
type: MGH
dimensions: 256 x 256 x 128
voxel sizes: 1.0000, 1.0000, 1.3300
type: SHORT (4)
fov: 256.000
dof: 0
xstart: -128.0, xend: 128.0
ystart: -128.0, yend: 128.0
zstart: -85.1, zend: 85.1
TR: 2000.00 msec, TE: 3.44 msec, TI: 900.00 msec, flip angle:
9.00 degrees
nframes: 1
PhEncDir: ROW
ras xform present
xform info: x_r = 0.5924, y_r = 0.0086, z_r = -0.8056, c_r =
-9.9942
: x_a = -0.7780, y_a = -0.2537, z_a = -0.5747, c_a =
13.5548
: x_s = 0.2093, y_s = -0.9672, z_s = 0.1436, c_s =
-22.2562
mri_normalize -noconform rawavg.mgz test.mgz
not interpolating and embedding volume to be 256^3...
reading from rawavg.mgz...
normalizing image...
MRInormInit:
Talairach origin at (142, 110, 71)
wsize 10, windows 14 above, 9 below
max gradient 1.000
.
.
.
mri_info test.mgz
Volume information for test.mgz
type: MGH
dimensions: 256 x 256 x 128
voxel sizes: 1.0000, 1.0000, 1.3300
type: SHORT (4)
fov: 256.000
dof: 0
xstart: -128.0, xend: 128.0
ystart: -128.0, yend: 128.0
zstart: -85.1, zend: 85.1
TR: 2000.00 msec, TE: 3.44 msec, TI: 900.00 msec, flip angle:
9.00 degrees
nframes: 1
PhEncDir: UNKNOWN
ras xform present
xform info: x_r = 0.5924, y_r = 0.0086, z_r = -0.8056, c_r =
-9.9942
: x_a = -0.7780, y_a = -0.2537, z_a = -0.5747, c_a =
13.5548
: x_s = 0.2093, y_s = -0.9672, z_s = 0.1436, c_s =
-22.2562
On Tue, 9 Nov 2010, Falk
Lüsebrink wrote:
Dear FreeSurfers,
The -noconform flag of mri_normalize doesn't seem to work properly in the
centos4_x86_64_stable-pub-v5.0.0 build. I have been trying to process a volume
with a native isotropic resolution of 0.7mm using recon-ll including the -cm
flag to conform the input to minimum. But during the normalization of
mri_normalize the volume is conformed to an isotropic resolution of 1mm.
The flag is correctly used during mri_normalize, but it doesn't seem to do
anything. The recon-all log says:
"not interpolating and embedding volume to be 256^3..."
But the output volume T1.mgz is conformed to 256^3 and therefore to an
isotropic resolution of 1mm. This also happens if mri_normalize is used by hand
using the -noconform flag.
A fix is highly appreciated.
Thanks in advance,
Falk Lüsebrink
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