you need to make sure that the direction cosines are correct. You can check whether it is correct by looking at it in tkmedit, ie,
tkmedit -f yourfile.nii It should look coronal in the coronal view, etc. If it is wrong, there's no easy way to fix it. I'd go back to the original dicoms if you can. doug Lisa F. Akiyama wrote: > Hi Doug, > > I was able to locate the original nifti files that contain all slices > in one file downloaded from NIHPediatrics. > > I was able to run : > > *recon-all -autorecon1 -notalairach -s 1433_1101 -i > $SUBJECTS_DIR/1433_1101/mri/orig/deface_1433_V1_t1w.nii -force* > > But the output file orientations are still rotated in a odd way. > Is there a way to fix these output orientations? > Listed below are the mri_info outputs for both the input and the > output files. I'll also attach the input and the output files. > > <INPUT FILE mri_info> > > type: nii > dimensions: 256 x 256 x 46 > voxel sizes: 0.9766, 0.9766, 3.0000 > type: FLOAT (3) > fov: 250.000 > dof: 0 > xstart: -125.0, xend: -125.0 > ystart: -125.0, yend: -125.0 > zstart: -69.0, zend: -69.0 > 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 = -11.5117 > : x_a = 0.0000, y_a = 1.0000, z_a = 0.0000, > c_a = 9.4883 > : x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, > c_s = -4.1000 > Orientation : RAS > Primary Slice Direction: axial > > voxel to ras transform: > 0.9766 0.0000 0.0000 -136.5116 > 0.0000 0.9766 0.0000 -115.5116 > 0.0000 0.0000 3.0000 -73.1000 > 0.0000 0.0000 0.0000 1.0000 > > voxel-to-ras determinant 2.86102 > > ras to voxel transform: > 1.0240 -0.0000 -0.0000 139.7879 > -0.0000 1.0240 -0.0000 118.2839 > -0.0000 -0.0000 0.3333 24.3667 > 0.0000 0.0000 0.0000 1.0000 > > > <OUTPUT FILE mri_info> > > type: MGH > dimensions: 256 x 256 x 256 > voxel sizes: 1.0000, 1.0000, 1.0000 > type: UCHAR (0) > fov: 256.000 > dof: 0 > xstart: -128.0, xend: 128.0 > ystart: -128.0, yend: 128.0 > zstart: -128.0, zend: 128.0 > 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 = -11.5116 > : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, > c_a = 9.4883 > : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, > c_s = -4.1000 > > talairach xfm : > > /usr/local/freesurfer/subjects/1433_v1_multinii/mri/transforms/talairach.xfm > Orientation : LIA > Primary Slice Direction: coronal > > voxel to ras transform: > -1.0000 0.0000 0.0000 116.4884 > 0.0000 0.0000 1.0000 -118.5117 > 0.0000 -1.0000 0.0000 123.9000 > 0.0000 0.0000 0.0000 1.0000 > > voxel-to-ras determinant -1 > > ras to voxel transform: > -1.0000 0.0000 0.0000 116.4884 > -0.0000 -0.0000 -1.0000 123.9000 > -0.0000 1.0000 -0.0000 118.5117 > 0.0000 0.0000 0.0000 1.0000 > > > > Thank you in advance. > > > Best, > Lisa Akiyama > ** > ______________________________ > Lisa F. Akiyama > Research Study Assistant > Institute for Learning & Brain Sciences (I-LABS) > University of Washington > > P Please consider the environment before printing this e-mail. > > > > On Fri, Oct 29, 2010 at 12:05 PM, Lisa F. Akiyama <lris...@uw.edu > <mailto:lris...@uw.edu>> wrote: > > Hi Doug, > > Thanks for the tips. I will look into putting all the slices into > one volume. > > > Best, > Lisa > ______________________________ > Lisa F. Akiyama > Research Study Assistant > Institute for Learning & Brain Sciences (I-LABS) > University of Washington > > P Please consider the environment before printing this e-mail. > > > > On Fri, Oct 29, 2010 at 11:53 AM, Douglas N Greve > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > You would have to take all 45 slices and put them into one > volume. It won''t work slice-by-slice. It is probably the case > that this won't work either as we usually use high res data. > For intensity normalization, maybe it will work. > > > doug > > Lisa F. Akiyama wrote: > > Hi Doug, > > There are approximately 40~45 slices of each individual's > brain, > each saved as separate nifti files. > I'm trying to use FreeSurfer for the Non-uniform intensity > normalization and skull strip functions. > So, if I edit the header of each nifti file so that the > slice thickness isn't 0, > recon-all -autorecon1 should work? > > Thanks. > > Best, > Lisa > > ______________________________ > Lisa F. Akiyama > Research Study Assistant > Institute for Learning & Brain Sciences (I-LABS) > University of Washington > > P Please consider the environment before printing this e-mail. > > > > On Fri, Oct 29, 2010 at 10:55 AM, Douglas N Greve > <gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>>> wrote: > > The problem is that the slice thickness is 0. BTW, I > don't know > what you are planning to do with this in freesurrfer, > but it's not > going to work with only one slice. > > > doug > > Lisa F. Akiyama wrote: > > Hi Doug, > > Here's the result of mri_info: > > ubuntu:~> mri_info > > $SUBJECTS_DIR/1433_v1/mri/orig/deface_1433_V1_t1w_slice0.nii > INFO: using NIfTI-1 qform > Volume information for > > > /usr/local/freesurfer/subjects//1433_v1/mri/orig/deface_1433_V1_t1w_slice0.nii > type: nii > dimensions: 256 x 256 x 1 > voxel sizes: 0.9766, 0.9766, 0.0000 > type: FLOAT (3) > fov: 250.000 > dof: 0 > xstart: -125.0, xend: -125.0 > ystart: -125.0, yend: -125.0 > zstart: -0.0, zend: -0.0 > 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 = -11.5117 > : x_a = 0.0000, y_a = -1.0000, z_a > = -0.0000, > c_a = 8.5118 > : x_s = 0.0000, y_s = 0.0000, z_s > = 1.0000, > c_s = -73.1000 > Orientation : RPS > Primary Slice Direction: axial > > voxel to ras transform: > 0.9766 0.0000 -0.0000 -136.5116 > 0.0000 -0.9766 -0.0000 133.5117 > 0.0000 0.0000 0.0000 -73.1000 > 0.0000 0.0000 0.0000 1.0000 > > voxel-to-ras determinant 0 > > ras to voxel transform: > mat = NULL! > MatrixFree: NULL mat POINTER! > > > Thank you. > > Best, > Lisa > ______________________________ > Lisa F. Akiyama > Research Study Assistant > Institute for Learning & Brain Sciences (I-LABS) > University of Washington > > P Please consider the environment before printing > this e-mail. > > > > On Thu, Oct 28, 2010 at 4:25 PM, Douglas N Greve > <gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>>>> wrote: > > mri_info *deface_1433_V1_t1w_slice0.nii > > > > -- Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > FileDrop: > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > > > 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. > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
