Hi,
I am trying to convert SPM5 .nii files into bshort and I used the following command:
mri_concat fkoch-0007*.nii --o bold/007/fspm_000.bshort
The command seems to work in that I have a bunch of bshort files in my bold/007 directory but when I try to view the slices (using sliceview-sess for example) the slices are all upside-down (rotated by 180 degrees). Is there an option I can use to get them the right side up?
I'm using FS v3 on an IntelMac and my version of mri_concat is stable3. Here is the output of bugr: ---------------------------------------------------------------------
FREESURFER_HOME: /Applications/freesurfer
Build stamp: freesurfer-Darwin-tiger-i686-stable-pub-v3.0.5
Kernel info: Darwin 8.11.1 i386
---------------------------------------------------------------------
Thanks, Leila