processing-scripts
28 Subscribers 
processing-scripts > 3dresample--RPI
Showing 1-2 of 2 posts
May 24, 2014 07:05 AM | xiufen zhang
3dresample--RPI
in the script 1_anatpreproc.sh it says
3dresample -orient RPI -inset ${anat}.nii.gz -prefix ${anat}_RPI.nii.gz，and this is for Reorient to fsl-friendly space.
however in the fcon_1000_Preprocessing.pdf it says
1. All datasets were oriented to RPI.
My question is why we do orient again?
how can we know the orient of a data?
3dresample -orient RPI -inset ${anat}.nii.gz -prefix ${anat}_RPI.nii.gz，and this is for Reorient to fsl-friendly space.
however in the fcon_1000_Preprocessing.pdf it says
1. All datasets were oriented to RPI.
My question is why we do orient again?
how can we know the orient of a data?
May 30, 2014 08:05 AM | Maarten Mennes
RE: 3dresample--RPI
Hello,
yes, all released data has been reoriented to RPI. Reorienting it again as per the script will not change anything. The script has the reorienting step so it will also work on data that was not downloaded through INDI or the fcon1000 (i.e., data you collected locally).
You can check the orientation with 3dinfo of fslhd or by opening it in fslview and checking the labels. However, I suggest to always check with your local MR physicist what orientation the data is in when it comes out of the scanner.
Maarten
yes, all released data has been reoriented to RPI. Reorienting it again as per the script will not change anything. The script has the reorienting step so it will also work on data that was not downloaded through INDI or the fcon1000 (i.e., data you collected locally).
You can check the orientation with 3dinfo of fslhd or by opening it in fslview and checking the labels. However, I suggest to always check with your local MR physicist what orientation the data is in when it comes out of the scanner.
Maarten