[Freesurfer] mri_convert, primary slice direction and resampling

2007-04-16 Thread Julia Hamstra
n 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 <[EMAIL PROTECTED]> wrote: Hi, Can mri_convert work with slice orientation other than axial? My input is sagittal (slices collected

[Freesurfer] mri_convert, primary slice direction and resampling

2007-04-16 Thread Julia Hamstra
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

[Freesurfer] mri_convert does not recognize dicom files

2006-12-22 Thread Julia Hamstra
Hello, I am unable to use mri_convert to import dicom files. Below are examples of the errors. For a GE scan: mri_convert -it ge -ot mgz -i 01.v2 -o orig.mgz reading from 01.v2... genesisRead(): can't determine file name format for ./01.v2 For a Siemens scan: mri_convert -it siemens_dicom -ot mg

[Freesurfer] mri_convert in 4D

2006-04-11 Thread Julia Hamstra
, 0.538951)writing to run.nii.gz...thanks~julia On 4/8/06, Bruce Fischl < [EMAIL PROTECTED]> wrote:how are you displaying it? And can you send the entire output? On Fri, 7 Apr2006, Julia Hamstra wrote:> Hi,> I am getting two errors when creating NIFTI files from dicoms using> mri_conv

[Freesurfer] mri_convert in 4D

2006-04-07 Thread Julia Hamstra
Hi, I am getting two errors when creating NIFTI files from dicoms using mri_convert. The first is that the 4D images are being spatially contactonated. It does not seem to be treating it as a timeseries. This is the command:  mri_convert -it dicom -ot nii s6761334/i6761335.MRDC.1 run.nii.gz Addi