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
Hi Kayle, can you try the following
bbregister --s SLOTS007 --mov flair.mgz --init-header --reg reg.test.dat --t2 --lta reg.test.lta
this should hopefully generate a good registration. If it does, then I can find a work-around for you doug
On 05/23/2014 03:05 PM, Kayle Sawyer wrote:
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Douglas N Greve -
Kayle Sawyer