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" <barrond@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 <greve@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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