That is the right mincost (you can also find it in the .mincost file),
and that cost is very good. Maybe too good. Make sure to look at the
registration.
I don't know why things are not changing when you left right reverse.
Try doing the flip with mri_convert
mri_convert lowb.nii lowb.lrrev.nii --left-right-reverse-pix
doug
On 7/11/13 7:14 PM, Barron, Daniel S wrote:
Hi Doug, sorry to email again.
I just tested the bbregister --surf-cost method by registering a
subject's 001.mgz (T1) with it's lowb.nii and lowbflipped.nii
(intentionally L-R flipped). They both gave me the same final cost
function, the 0.2305 highlighted below.
I verified that the lowbflipped is flipped in Mango: lowb.nii is
X+,Y-,Z+; lowbflipped.nii is X-,Y-,Z+. However, mri_info says the
orientation for both is RPS. I am not sure what this means.
Please help,
Daniel
On Jul 11, 2013, at 5:58 PM, "Barron, Daniel S"
<barr...@livemail.uthscsa.edu <mailto:barr...@livemail.uthscsa.edu>>
wrote:
Hi Doug, thanks for the tip. I'm making a script to go in and grab
the final cost from each subject's registration and display it in a
table. Just to make sure, have I highlighted the correct Cost
function below? This is from the log file produced by bbregister
--surf-cost
Thanks again, Daniel
….
Writing lh cost to /Volumes/barrond/NYU/FreeSurfer/NC001/final.lh.mgh
Writing rh cost to /Volumes/barrond/NYU/FreeSurfer/NC001/final.rh.mgh
Number of iterations 5
Min cost was 0.230545
Number of FunctionCalls 376
TolPowell 0.000000
nMaxItersPowell 36
OptimizationTime 32.851000 sec
Parameters at optimum (transmm) -0.08284 -0.07071 -0.02021
Parameters at optimum (rotdeg) 0.19036 -0.00484 0.26953
Writing lh cost to /Volumes/barrond/NYU/FreeSurfer/NC001/final.lh.mgh
Writing rh cost to /Volumes/barrond/NYU/FreeSurfer/NC001/final.rh.mgh
Final costs ----------------
Number of surface hits 279254
WM Intensity 880.2007 +/- 244.9590
Ctx Intensity 1084.7520 +/- 284.4271
Pct Contrast 20.3801 +/- 22.2371
Cost 0.2305 <-----Is this the right one??
RelCost 0.2309
….
On Jul 11, 2013, at 4:41 PM, Douglas N Greve
<gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>>
wrote:
you can run bbregister using the b=0 image as input. The final cost
function value should beless than .9, if it is more than that then it
probably means you have an LR flip.
doug
On 07/11/2013 03:52 PM, Barron, Daniel S wrote:
Dear Freesurfers,
I am trying to perform probabilistic tractography (FSL Probtrackx)
between seed and target VOIs made with Freesurfer's recon-all (T1)
and dt_recon (DW) pipelines.
I have the original T1 DICOMs, however, I only have the DW NIFTI
image volumes. I do not know how the DW DICOMS were converted to
NIFTI and am worried about L-R flipping.
Within Mango, I have found the T1 images converted with mri_convert
are (X+,Y-,Z+). The DW NIFTI is (Y-,Z-,X-). mri_info gives me a
lot of information that, unfortunately, I do not entirely understand.
Can you recommend a way for me to verify consistent orientation in
both my T1 and DW images? Thank you!
Cheers,
Daniel
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