Hello,

I'm having an issue w/ TLRCing my images. There doesn't appear to be a place to upload screenshots anymore, so I'll try to explain things as best as possible.

The command I am using is this--the same command I have always used:
@auto_tlrc -no_ss -base ~/abin/TT_N27+tlrc -input 2H_T2_CardANATrai_SS+orig

If I view the anatomical before running the above script, it is plumb in all directions. However, after running the script, the axial view seems rotated to the right by about 15 degrees. This happens to all my data from this particular dataset, so there must be something funky going on that I'm not aware of.

For this dataset, we did have to deoblique it (3drefit -deoblique) and resample is to RAI space using 3dresample, things we usually don't have to do in our standard pipeline. If I do a 3dinfo, everything in the header looks good, i.e. it's plumb and in RAI space on both the ORIG image and the TLRC image.
3dWarp -deoblique -prefix ${subj}_T2_CardANAT ${subj}_T2anatomy.hdr
3dresample -orient rai -prefix ${subj}_T2_CardANATrai -inset ${subj}_T2_CardANAT+orig

Any thoughts as to what's going on?

Thanks in advance for your time!
chris



Edited 1 time(s). Last edit at 07/12/2012 10:58PM by kafkaskid415.