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 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 |
SIEMENS MAGNETOM ConnectomA syngo MR D11
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\\USER\INVESTIGATORS\Oscar-Berman\SLOTS\t2_spc_da-fl_sag_p2_iso_0.9
TA:5:47 PAT:2 Voxel size:0.4Ã0.4Ã0.9 mm Rel. SNR:1.00 :spcir
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Properties
Prio Recon Off
Before measurement
After measurement
Load to viewer On
Inline movie Off
Auto store images On
Load to stamp segments Off
Load images to graphic segments Off
Auto open inline display Off
Wait for user to start Off
Start measurements single
Routine
Nr. of slab groups 1
Slabs 1
Position L0.0 A4.3 F18.2 mm
Orientation Sagittal
Phase enc. dir. A >> P
AutoAlign Head > Brain
Phase oversampling 0 %
Slice oversampling 0.0 %
FoV read 230 mm
FoV phase 100.0 %
Slice thickness 0.90 mm
TR 5000 ms
TE 389.0 ms
Concatenations 1
Filter Raw filter, Normalize
Coil elements BOT;TOP
Contrast
MTC Off
Magn. preparation T2 sel. IR
TI 1800 ms
Fat suppr. None
Water suppr. None
Restore magn. Off
Measurements 1
Reconstruction Magnitude
Multiple series Each measurement
Resolution
Base resolution 256
Phase resolution 100 %
Phase partial Fourier Allowed
Interpolation On
PAT mode GRAPPA
Accel. factor PE 2
Ref. lines PE 24
Reference scan mode Integrated
Image Filter Off
Distortion Corr. Off
Accel. factor 3D 1
Prescan Normalize Off
Normalize On
B1 filter Off
Raw filter On
Intensity Weak
Slope 25
Elliptical filter Off
Slice resolution 80 %
Slice partial Fourier 7/8
Geometry
Nr. of slab groups 1
Slabs 1
Position L0.0 A4.3 F18.2 mm
Phase enc. dir. A >> P
Phase oversampling 0 %
Slice oversampling 0.0 %
Slices per slab 192
Series Interleaved
Nr. of sat. regions 0
Position mode L-P-H
Fat suppr. None
Water suppr. None
Special sat. None
Special sat. None
Table position P
Restore magn. Off
System
Body Off
TOP On
BOT On
Position mode L-P-H
Positioning mode REF
Table position H
Table position 0 mm
MSMA S - C - T
Sagittal R >> L
Coronal A >> P
Transversal F >> H
Save uncombined Off
Coil Combine Mode Adaptive Combine
AutoAlign Head > Brain
Auto Coil Select Off
Shim mode Standard
Adjust with body coil Off
Confirm freq. adjustment Off
Assume Dominant Fat Off
Assume Silicone Off
Adjustment Tolerance Auto
? Ref. amplitude 1H 0.000 V
Position L0.0 A4.3 F18.2 mm
Rotation 0.00 deg
F >> H 230 mm
A >> P 230 mm
R >> L 173 mm
Frequency 1H 123.256797 MHz
Correction factor 1
SLoopIRnsHT1 1H 515.179 V
! Gain High
Table position 0 mm
Img. Scale. Cor. 1.000
Physio
1st Signal/Mode None
Trigger delay 0 ms
Magn. preparation T2 sel. IR
TI 1800 ms
Dark blood Off
Resp. control Off
Inline
Distortion correction Off
Sequence
Introduction On
Dimension 3D
Elliptical scanning Off
Reordering Linear
Bandwidth 751 Hz/Px
Flow comp. No
Allowed delay 30 s
Echo spacing 3.35 ms
Adiabatic-mode Off
Turbo factor 278
Echo train duration 851
RF pulse type Normal
Gradient mode Fast
Excitation Non-sel.
Flip angle mode T2 var
TX/RX delta frequency 0 Hz
TX Nucleus None
TX delta frequency 0 Hz
Coil elements BOT;TOP
Acquisition duration 0 ms
Organ under exam. None
BOLD
Subtract Off
Save images On
Autoscaling Off
Scaling factor 1
Offset 0
Subtrahend 1
Subtraction indices
StdDev Off
Std-Dev-Sag Off
Std-Dev-Cor Off
Std-Dev-Tra Off
Std-Dev-Time Off
MIP-Sag Off
MIP-Cor Off
MIP-Tra Off
MIP-Time Off
Radial MIP Off
Save original images On
Distortion Corr. Off
Save original images On
Number of radial views 1
Axis of radial views L-R
MPR Sag Off
MPR Cor Off
MPR Tra Off _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
