can you try running recon-all directly on the dicoms? Also, it's probably pretty noisy at .5mm in-plane - how does it look? Is it whole brain?
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
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.