================== README: GROUP3 ========================

#### General
This group contains images from 13 patients instead of 14. Patient #13 did not
have any post-operative MRI, only a post-operative CT. Patient #13 is therefore
not included in this group. No validation tags are provided for this group.


#### Each directory contains:

1) preop MRI in scanner space

2) postop MRI in scanner space

3) tumor mask for preop MRI. Some cases have special masks
       - case #02: one mask with the tumor on which the operation was done and
         the other mask with the tumors in both hemispheres.
       - case #05: one mask with the tumor only and the other including the previous resection cavity.
       - case #10: this mask contains two different labels (intensity values), one for the enhancing tumor and another for the non-enhancing tumor. 

4) xfm file to transform the preop MRI into ultrasound space. 
   This way the preop MRI and US from group 1 can be viewed in the same frame of reference. 
   To apply the xfm file to the preop MRI you could do:
   mincresample preop_mri.mnc -transform transform.xfm preop_mri_in_US_space.mnc -tfm
   

#### Tips to manipulate the data:

To register the pre-operative MRI with the post-operative MRI you can use mritoself or minctracc. 
If the heads were placed very differently in the scanner, it might be necessary to first do a quick manual 
registration by choosing 4 homologous landmarks using register.

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To view the preop MRI with the corresponding tumor mask:
register 01_preop_mri.mnc 01_tumor.mnc

Then if the tumor window appears all black, change the dynamic range: click Type 2 instead of 250 as the
maximum.