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>> 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>>> 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> > 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. > > -- 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
