1 Nov
2010
1 Nov
'10
2:32 p.m.
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 1.0000Thank 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 <lrisa87@uw.edu mailto:lrisa87@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 <greve@nmr.mgh.harvard.edu <mailto:greve@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 <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@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 <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>> wrote: mri_info *deface_1433_V1_t1w_slice0.nii -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@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 greve@nmr.mgh.harvard.edu <mailto:greve@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
greve@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