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.edumailto: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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