Hi Liang,
you need to use the monkey analysis stream as many of the steps simply don't apply to nonhuman data (such as the automated Talairach alignment!)
cheers Bruce On Wed, 17 Nov 2010, liang wang wrote:
Hi Bruce,
I had tried to run recon-all on the dicoms. But the same errors show up. This image covering whole brain is obtained (Siemens 3T) actually from a monkey and looks good. Here is the header information from the dicom image. According to the suggestion in Freesurfer FAQ, I run "tkregister2 --mgz --s subj --fstal". Surprisingly, a strange image appears and looks a white line. Seemingly the brain image is rotated to a invisible orientation. Any suggestions?
Best, Liang
#------------------------------------------- Volume information for 001.mgz type: MGH dimensions: 256 x 256 x 160 voxel sizes: 0.5000, 0.5000, 1.0000 type: SHORT (4) fov: 160.000 dof: 0 xstart: -64.0, xend: 64.0 ystart: -64.0, yend: 64.0 zstart: -80.0, zend: 80.0 TR: 2500.00 msec, TE: 4.38 msec, TI: 1100.00 msec, flip angle: 8.00 degrees nframes: 1 PhEncDir: ROW 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 = -0.0000, z_a = -1.0000, c_a = 6.9217 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = -1.3494
talairach xfm : Orientation : LIP Primary Slice Direction: coronal
voxel to ras transform: -0.5000 -0.0000 -0.0000 66.6988 -0.0000 -0.0000 -1.0000 86.9217 0.0000 -0.5000 0.0000 62.6506 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 -0.0000 -2.0000 125.3012 0.0000 -1.0000 0.0000 86.9217 0.0000 0.0000 0.0000 1.0000
2010/11/17 Bruce Fischl fischl@nmr.mgh.harvard.edu
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.