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 ca
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
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 approxima
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-a
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/ori
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
There is something wrong with the header of that nifti file. Can you
send the result of:
mri_info *deface_1433_V1_t1w_slice0.nii
doug
*
Lisa F. Akiyama wrote:
> Hello FreeSurfers,
>
> I am trying to run autorecon-1 on data (nifti) downloaded from the NIH
> MRI Study of Normal Brain Development
Hello FreeSurfers,
I am trying to run autorecon-1 on data (nifti) downloaded from the NIH MRI
Study of Normal Brain Development (Pediatric MRI Study) Repository.
However, the command exited with errors mentioning that the source matrix
has a zero determinant.
I've read past e-mail conversations on
