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 <fis...@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 <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. 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