Hi Tyler, Doug can correct me if I'm wrong, but I believe if you use the --spm-nii option it will fix this.
Cheers, Michael On Mon, Mar 28, 2011 at 1:47 PM, Tyler Seibert <tseib...@ucsd.edu> wrote: > Screenshot2 attached > > > ---------- Forwarded message ---------- > From: Tyler Seibert <tseib...@ucsd.edu> > Date: Thu, Mar 17, 2011 at 4:02 PM > Subject: bbregister bug? with init-spm option--flips left and right > To: freesurfer@nmr.mgh.harvard.edu > > > Hello, > > I hope this is the correct email list--this is my first time posting (just > subscribed). > > I have been using bbregister to calculate a tranformation matrix between a > T2 image (T2brain.nii.gz) and the subject's T1.mgz for subsequent use with > mri_vol2surf. I have found that the init-fsl option frequently gives very > poor registrations (e.g., registered T2 is rotated 30+ degrees from T1). The > init-spm option seemed to be working great. However, upon close inspection, > I became suspicious this option was actually flipping the T2 so that the > left hemisphere became right and vice versa. I am using FreeSurfer version > 4.5 and have spm8 referenced in my matlab path. > > I used a directory ~/bbreg_test in my home directory for the test (linux), > which consisted simply of running bbregister with init-fsl and init-spm > options. The attached log file (log.txt) contains the commands I used. The > terminal output from each test was saved in text files as well, also > attached. > > I have also attached two screenshots of the tkregister2 output for these > tests. In each screenshot the far left image is the registered T2 using > init-spm, and the far right image is the registered T2 using init-fsl. As > the init-fsl version is clearly wrong, the middle image in each screenshot > is the init-fsl output again, but manually rotated several degrees to the > left to better emphasize the mirror-image relationship between the init-spm > (far left) and init-fsl (middle and far right) output images. > > Please let me know if there is anything further you need from me to > investigate this or if there is any insight you can give me as far as how to > avoid this error. I noticed at line 209 of the spm_test.txt log file there > is a message stating that RAS coordinate system is assumed (see below, where > I have copied lines 208-213 for convenience). This may very well be the > problem, as the T2brain.nii.gz volume is in LAS, according to mri_info > output. However, I do not see where I can override this RAS assumption. > > >> >> >> >> >> >> >> >> >> /home/tylers/apps/spm8/spm_coreg.m >> >> >> >> >> >> INFO: Assuming RAS coordinate system >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> using >> /home/tylers/bbreg_test/init-spm/tmp.bbregister.15515/spmregister/refvol.spmregister.img >> as the target image >> >> using >> /home/tylers/bbreg_test/init-spm/tmp.bbregister.15515/spmregister/movvol.spmregister.img >> as the source image >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> > > Thank you, > > -- > Tyler Seibert > > Dept. of Bioengineering > Medical Scientist Training Program > University of California, San Diego > > > > -- > Tyler Seibert > > Dept. of Bioengineering > Medical Scientist Training Program > University of California, San Diego > > > _______________________________________________ > 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. > >
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