Hello,

We have been examining the pial surface adjustment with FLAIR scans, and the improvement is quite dramatic. There are MANY areas where the pial surface was clearly wrong and has been substantially improved, considerably reducing (often eliminating) the need for manual pial corrections. I suggest everyone who uses FreeSurfer surfaces acquire a FLAIR scan if they can (see attached for the sequence we’re using). 

However, for most of our participants, we have run into a serious problem with bbregister.

We're running recon-all with two input volumes:
-i MEMPRAGE_scan -FLAIR FLAIR_scan

Recon-all completes successfully, however the results do not look good due to a bad 'bbregister' registration step.

The MEMPRAGE and FLAIR runs were acquired within the same scanning session and they're very well registered to begin with. However, the 'bbregister' step seems to not work well, and they end up grossly misaligned.

Here is an example (on the Martinos network):
[kslays@ficus ~]$
source /usr/local/freesurfer/nmr-stable53-env;
setenv SUBJECTS_DIR /autofs/space/ficus_004/users/SLOTS_subjects;
cd $SUBJECTS_DIR;

recon-all -all -subjid SLOTS007 \
    -i         $SUBJECTS_DIR/SLOTS007/3danat/006/MEMPRAGE_RMS.mgz \
    -FLAIR     $SUBJECTS_DIR/SLOTS007/flair/007/flair.mgz \
    -FLAIRpial -mprage -3T -pctsurfcon -qcache -hippo-subfields


Check input volume registration (looks good):

tkregister2 --targ SLOTS007/mri/orig/001.mgz \
           --mov  SLOTS007/mri/orig/FLAIRraw.mgz \
           --reg NULL --regheader

Check bbregister output (looks bad):

tkregister2 --mov SLOTS007/mri/orig/FLAIRraw.mgz \
           --reg SLOTS007/mri/transforms/FLAIRraw.dat --surf

How do we correct the bbregister step? 

Thanks in advance for your input.
-Kayle

P.S. If you would like to see other examples, feel free to look at other recons in the same directory. Here is an example where bbregister worked, and the pial corrections are dramatic:
freeview -v SLOTS005/mri/FLAIR.mgz            \
-f SLOTS005/surf/lh.white:edgecolor=yellow    \
SLOTS005/surf/rh.white:edgecolor=yellow       \
SLOTS005/surf/lh.pial:edgecolor=red           \
SLOTS005/surf/rh.pial:edgecolor=red           \
SLOTS005/surf/lh.woFLAIR.pial:edgecolor=green \
SLOTS005/surf/rh.woFLAIR.pial:edgecolor=green \
-ras -37 -46 -42 



Kayle Sawyer, PhD

Athinoula A. Martinos Center for Biomedical Imaging
MGH East Campus, Charlestown Navy Yard
Building 149, South Central 1113 - Seat F
149 13th Street
Boston, MA 02129
OFFICE:(617) 726-8791

Laboratory of Neuropsychology
Boston University School of Medicine L-815
72 E. Concord St
Boston, MA 02118
OFFICE:(617) 638-4803

VA Boston Healthcare System Jamaica Plain
150 South Huntington Ave 151-A, D11-126
Boston, MA 02130
OFFICE:(857) 364-4003
FAX:   (857) 364-5829