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 <fis...@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. >> >> > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
