Software - Multiple Atlas Brain Extraction (ICC)
This is a multiple atlas skull stripping application that works on T1 images to remove the skull. A pre defined set of atlases is taken and each atlas is rigidly, then affinely registered to the image of interest. Then using diffeomorphic demons, non-rigid registration is performed to the target image. The resulting non-rigid transform is then used to warp the ICC mask defined on the atlas to the image of interest space. Finally using a procedure known as STAPLE (Simultaneous Truth And Performance Level Estimation), the most likely ICC segmentation is iteratively computed. The stripped brain is then "stamped" out using this ICC mask.
For minor cleanups we use a version of the slice viewer that displays the stripped brain overlaid in color on the whole head image. A brush of adjustable size can then either erase small areas that jut from the brain or restore small chunks that have been mistakenly removed during the skullstrip.
 |
 |
|
Figure Multi-Atlas Brain Extraction. Left: unstripped image. Right: stripped image after automated stage and minor user cleanup. |
|
Warning: date() [function.date]: It is not safe to rely on the system's timezone settings. You are *required* to use the date.timezone setting or the date_default_timezone_set() function. In case you used any of those methods and you are still getting this warning, you most likely misspelled the timezone identifier. We selected 'UTC' for 'UTC/0.0/no DST' instead in /var/www/html/software/skullstripicc_counter.php on line 88
Warning: date() [function.date]: It is not safe to rely on the system's timezone settings. You are *required* to use the date.timezone setting or the date_default_timezone_set() function. In case you used any of those methods and you are still getting this warning, you most likely misspelled the timezone identifier. We selected 'UTC' for 'UTC/0.0/no DST' instead in /var/www/html/software/skullstripicc_counter.php on line 63
Warning: fopen(./counter/skullstripicc_ip.txt) [function.fopen]: failed to open stream: Permission denied in /var/www/html/software/skullstripicc_counter.php on line 17
Warning: fwrite() expects parameter 1 to be resource, boolean given in /var/www/html/software/skullstripicc_counter.php on line 19
Warning: fclose() expects parameter 1 to be resource, boolean given in /var/www/html/software/skullstripicc_counter.php on line 20
Warning: fopen(./counter/skullstripicc_ip.txt) [function.fopen]: failed to open stream: Permission denied in /var/www/html/software/skullstripicc_counter.php on line 24
Warning: fwrite() expects parameter 1 to be resource, boolean given in /var/www/html/software/skullstripicc_counter.php on line 26
Warning: fclose() expects parameter 1 to be resource, boolean given in /var/www/html/software/skullstripicc_counter.php on line 27
Warning: fopen(./counter/skullstripicc_count.txt) [function.fopen]: failed to open stream: Permission denied in /var/www/html/software/skullstripicc_counter.php on line 17
Warning: fwrite() expects parameter 1 to be resource, boolean given in /var/www/html/software/skullstripicc_counter.php on line 19
Warning: fclose() expects parameter 1 to be resource, boolean given in /var/www/html/software/skullstripicc_counter.php on line 20
Warning: date() [function.date]: It is not safe to rely on the system's timezone settings. You are *required* to use the date.timezone setting or the date_default_timezone_set() function. In case you used any of those methods and you are still getting this warning, you most likely misspelled the timezone identifier. We selected 'UTC' for 'UTC/0.0/no DST' instead in /var/www/html/software/skullstripicc_counter.php on line 76
Warning: fopen(./counter/skullstripicc_visit_log.txt) [function.fopen]: failed to open stream: Permission denied in /var/www/html/software/skullstripicc_counter.php on line 24
Warning: fwrite() expects parameter 1 to be resource, boolean given in /var/www/html/software/skullstripicc_counter.php on line 26
Warning: fclose() expects parameter 1 to be resource, boolean given in /var/www/html/software/skullstripicc_counter.php on line 27
1260 unique visits since June 1, 2006