Hi, Can mri_convert work with slice orientation other than axial? My input is sagittal (slices collected from right to left), but when I create files from mri_convert the header reads axial. This is particularly problematic when converting to analyze format from dicoms or another file type because the dimensions of the sagittal slices are applied the transverse plane.
Using in_orientation and out_orientation options, the images will display correctly, but the header still reads axial.
Can mri_convert subsample an image by retaining every other voxel without interpolating between voxels?
Thank you, ~julia
To more fully explain the road block, this is the output of 'mri_info analyzefile --slicedirection'
MatlabRead: readHeader returned NULL
WARNING: analyzeRead(): matfile analyzefile.mat exists but could not read ... may not be matlab4 mat file ... proceeding without it. ----------------------------------------------------------------- INFO: could not find analyzefile.mat file for direction cosine info. INFO: use Analyze 7.5 hdr->hist.orient value: 0, transverse unflipped (default). INFO: if not valid, please provide the information in analyzefile.mat file
I am running on a Mac. Does this have anything to do with it? I don't have matlab on the mac, but on a windows virtual machine.
thanks ~julia
On 4/16/07, Julia Hamstra jhamstra@gmail.com wrote:
Hi, Can mri_convert work with slice orientation other than axial? My input is sagittal (slices collected from right to left), but when I create files from mri_convert the header reads axial. This is particularly problematic when converting to analyze format from dicoms or another file type because the dimensions of the sagittal slices are applied the transverse plane.
Using in_orientation and out_orientation options, the images will display correctly, but the header still reads axial.
Can mri_convert subsample an image by retaining every other voxel without interpolating between voxels?
Thank you, ~julia
What happened to the .mat file? mri_convert should work with all orientations.
Julia Hamstra wrote:
To more fully explain the road block, this is the output of 'mri_info analyzefile --slicedirection'
MatlabRead: readHeader returned NULL
WARNING: analyzeRead(): matfile analyzefile.mat exists but could not read ... may not be matlab4 mat file ... proceeding without it.
INFO: could not find analyzefile.mat file for direction cosine info. INFO: use Analyze 7.5 hdr->hist.orient value: 0, transverse unflipped (default). INFO: if not valid, please provide the information in analyzefile.mat file
I am running on a Mac. Does this have anything to do with it? I don't have matlab on the mac, but on a windows virtual machine.
thanks ~julia
On 4/16/07, Julia Hamstra <jhamstra@gmail.com mailto:jhamstra@gmail.com> wrote:
Hi, Can mri_convert work with slice orientation other than axial? My input is sagittal (slices collected from right to left), but when I create files from mri_convert the header reads axial. This is particularly problematic when converting to analyze format from dicoms or another file type because the dimensions of the sagittal slices are applied the transverse plane. Using in_orientation and out_orientation options, the images will display correctly, but the header still reads axial. Can mri_convert subsample an image by retaining every other voxel without interpolating between voxels? Thank you, ~julia-- UC Davis Neuroscience Graduate Group The M.I.N.D. Institute - Amaral Lab (916) 703-0376
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