fsImportUsingMRIConvert.sh

(Note: This page is automatically generated. Please do not attempt to edit it!)

This script will import data into the standard FreeSurfer directory structure.
In contrast to fsImport.sh, this does NO re-orientation. It just runs FreeSurfers
own mri_convert program on both the image and the brain mask.

This script would be most useful for people who have already been doing some SPM/VBM
and have already got their nifti images in the correct orientation.

Usage: fsImportUsingMRIConvert.sh dataFile [ options ]
 
Mandatory Arguments:

  dataFile      : A file containing your patient names and details, like this:

                  Patient Mask                      Image            Image            Image             etc.
                  ALLFR   Nic_02979_1140620563.nii  02979-002-1.nii  02979-002-2.nii  02979-002-3.nii   etc.
                  ALLHA   Nic_03920_1351234123.nii  03929-002-1.nii  03929-003-1.nii  03929-004-1.nii   etc.

                  The first line is just text, and hence skipped.
                  
                  After that, you can use absolute or relative pathnames, using full filenames (including extension like .nii).
                  
                  Also, if the -noMask option is specified, then all images are assumed to be T1 scans, not brain masks.
                  The DRC default is to use a brain mask.
Options:


  -b beginRow   : is the start row in the dataFile.
  -e endRow     : is the end row in the dataFile.
  
  -noMask       : the first image is to be treated as a T1 scan, not a brain mask

  -M            : options to pass to mri_convert specified in double quotes