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
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On Fri, Oct 29, 2010 at 10:55 AM, Douglas N Greve <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>>> 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> 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> 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.