On Wed, 17 Nov 2010, liang wang wrote:
Hi Bruce,
I run the command on a NIFTI image converted by dicom files. The image can
be skull stripped using bet in FSL, but some skulls were not removed
clearly. Here is the information by mri_info. It seems to me normal, but
several scan parameters loss. For the nifti image, I use to3d (AFNI code) to
convert DICOM to nifti format and use 3drefit to fix up correctly the
orientation.
#-----------------------------------
type: nii
dimensions: 256 x 256 x 160
voxel sizes: 0.5000, 0.5000, 1.0000
type: SHORT (4)
fov: 128.000
dof: 0
xstart: -64.0, xend: -64.0
ystart: -64.0, yend: -64.0
zstart: -80.0, zend: -80.0
TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00
degrees
nframes: 1
PhEncDir: UNKNOWN
ras xform present
xform info: x_r = 1.0000, y_r = -0.0000, z_r = -0.0000, c_r =
-2.6988
: x_a = -0.0000, y_a = -1.0000, z_a = -0.0000, c_a =
-1.3494
: x_s = 0.0000, y_s = 0.0000, z_s = -1.0000, c_s =
6.9217
Orientation : RPI
Primary Slice Direction: axial
voxel to ras transform:
0.5000 -0.0000 -0.0000 -66.6988
-0.0000 -0.5000 -0.0000 62.6506
0.0000 0.0000 -1.0000 86.9217
0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant 0.25
ras to voxel transform:
2.0000 -0.0000 -0.0000 133.3976
0.0000 -2.0000 0.0000 125.3012
0.0000 0.0000 -1.0000 86.9217
0.0000 0.0000 0.0000 1.0000
2010/11/17 Bruce Fischl <fischl@nmr.mgh.harvard.edu>
wow, that's a completely wacky talairach xform. Did you run this straight
on the dicom images? The talairach clearly failed for some reason. Try
running mri_info on the dicoms to see if there is something strange in them
On Wed, 17 Nov 2010, liang wang wrote:
Hi FSusers,
The terminal displays errors when I run "recon-all -autorecon1 -subjid
..."
to get a skull-stripped brain image. The processing exits with the
following
errors regarding talairach transformation. Here is the talairach.xfm:
MNI Transform File
% tkregister2
Transform_Type = Linear;
Linear_Transform =
39.07553864 15.93667889 -36.86604309 -1474.05761719
1861.34423828 844.27008057 -1897.87268066 -75416.71093750
-606.90667725 -274.30368042 622.14581299 24711.26757812 ;
Any suggestions would be appreciated.
Best,
Liang
#--------------------------------------------------------------------
#@# Talairach Failure Detection Wed Nov 17 10:15:36 EST 2010
/mnt/cd/kastner/liang/resting_state/ph_062210/fs_skull/ph/mri
talairach_afd -T 0.005 -xfm transforms/talairach.xfm
ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm
***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050)
Linux node37.cluster 2.6.18-128.el5 #1 SMP Wed Jan 21 10:41:14 EST 2009
x86_64 x86_64 x86_64 GNU/Linux
recon-all -s ph exited with ERRORS at Wed Nov 17 10:15:36 EST 2010
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