Hi Zhennan if you run recon-all on any dataset it will create an example for you. The talairach.m3z maps the volume into the atlas coords. If it is oriented incorrectly then that would explain your problem. You can also use mri_info to see the direction cosines of the various volumes
cheers Bruce On Sat, 16 Feb 2013, Zhennan Yan wrote: > Dear Bruce, > > Thank you very much for your suggestions. I have fixed the reslicing problem > and I am still trying to use mri_ca_label to relabel sub-cortical structures > in my data. Now the program output a new seg, but the display of "tkmedit > mysubj norm.mgz -segmentation new_seg.mgz > $FREESURFER_HOME/FreeSurferColorLUT.txt" showed the orientation wrong (upside > down and maybe left-right fliped). This is very weird since I have used > "tkmedit mysubj norm.mgz -segmentation old_seg.mgz > $FREESURFER_HOME/FreeSurferColorLUT.txt" to confirm that old_seg.mgz has the > same orientation with norm.mgz. Do you have any idea about this? What's the > function of "transforms/talairach.m3z" in mri_ca_label? Could you please send > me a simple example T1, init_seg and relabeled result archived by > mri_ca_label? > Thanks! > > Best, > Zhennan > > Zhennan Yan > Department of Computer Science > Rutgers University > > On 2/1/2013 7:44 PM, Bruce Fischl wrote: >> that might be the problem. Specify nearest nbr resampling with -rt nearest >> on the mri_convert cmd line >> >> cheers >> Bruce >> >> On Fri, 1 Feb 2013, Zhennan Yan wrote: >> >>> Dear Bruce, >>> >>> I have mapped my labels to the Freesurfer labels. But when I tried the >>> "mri_ca_label -R init_label.mgz norm.mgz transforms/talairach.m3z >>> $FREESURFER_HOME/average/RB_all_2008-03-26.gca new_label.mgz", I got a >>> "Segmentation fault" after "0 singular and 1812 ill-conditioned covariance >>> matrices regularized". >>> I noticed that my initial segmentation image is not 255 cubed and has only >>> 30+ different subcortical labels (for example labels >>> 0,2,3,4,5,7,8,10,...,60,62). Then I tried to use the command "mri_convert >>> init_label.mgz init_label_c.mgz --conform" to conform it. But the output >>> init_label_c.mgz is not as I expected. I guess the reslicing interpolation >>> might introduce some "new labels" to my initial segmentation? >>> >>> My question is do I need to conform the initial seg into 255 cubed image? >>> How can I do this in my case? And what do you think is the problem cause >>> the failure of the mri_ca_label? >>> >>> Thanks! >>> Zhennan >>> >>> Zhennan Yan >>> Department of Computer Science >>> Rutgers University >>> >>> On 2/1/2013 10:28 AM, Bruce Fischl wrote: >>>> thanks Zhennan >>>> >>>> good luck and let us know if we can help >>>> Bruce >>>> On Fri, 1 Feb 2013, Zhennan Yan wrote: >>>> >>>>> Dear Bruce, >>>>> >>>>> Thank you for your help and the great work on Freesurfer! >>>>> >>>>> Best, >>>>> Zhennan >>>>> >>>>> Zhennan Yan >>>>> Department of Computer Science >>>>> Rutgers University >>>>> >>>>> On 1/31/2013 1:43 PM, Bruce Fischl wrote: >>>>>> 1. 40 subjects, 10 young, 10 middle ages, 10 elderly (healthy) and 10 >>>>>> with AD. >>>>>> >>>>>> 2. Many small things, the big one (described in our 2004 paper) is that >>>>>> we now use a nonlinear warp >>>>>> >>>>>> 3. Yes, hydrocephalus for example is hard, although we have made recent >>>>>> improvements in the warping that handle enlarged ventricles much better >>>>>> >>>>>> cheers >>>>>> Bruce >>>>>> >>>>>> >>>>>> On Thu, 31 Jan 2013, Zhennan Yan wrote: >>>>>> >>>>>>> Dear Bruce, >>>>>>> >>>>>>> Thank you very much for your reply. >>>>>>> I can convert my labels to Freesurfer labels and try the mri_ca_label >>>>>>> now. May I ask some more questions? >>>>>>> >>>>>>> 1) What subjects were used to train the atlas in the current version? >>>>>>> Were they healthy or diseased subjects? >>>>>>> 2) How the current implementation differs from the one in your Whole >>>>>>> Brain Segmentation (2002) paper? >>>>>>> 3) Is there any cases, e.g. on which clinical diseases, FreeSurfer >>>>>>> will produce less than ideal results? >>>>>>> >>>>>>> Thanks! >>>>>>> >>>>>>> Best, >>>>>>> Zhennan >>>>>>> >>>>>>> Zhennan Yan >>>>>>> Department of Computer Science >>>>>>> Rutgers University >>>>>>> >>>>>>> On 1/30/2013 3:10 PM, Bruce Fischl wrote: >>>>>>>> Hi Zhennan >>>>>>>> >>>>>>>> there is an option to mri_ca_label to read in a prior segmentation >>>>>>>> and >>>>>>>> iterate the MRF minimization, but unless your labels and conventions >>>>>>>> are >>>>>>>> identical to our's it's unlikely to work. You can use mri_ca_train >>>>>>>> to >>>>>>>> build the MRF and likelihoods and such if you want. >>>>>>>> >>>>>>>> cheers >>>>>>>> Bruce >>>>>>>> >>>>>>>> >>>>>>>> On Wed, 30 Jan 2013, Zhennan Yan wrote: >>>>>>>> >>>>>>>> > Dear freesurfer experts, >>>>>>>> > > I have questions about the MRF in Freesurfer: >>>>>>>> > (1) I have a T1 image and sub-cortical segmentation for it (nifti >>>>>>>> > format). But the segmentation is not perfect >>>>>>>> > and I would like to relabel it using the ICM algorithm as shown in >>>>>>>> fig.8 > in paper: Whole Brain Segmentation: >>>>>>>> > Automated Labeling of Neuroanatomical Structures in the Human >>>>>>>> Brain, > Fischl et al., (2002). >>>>>>>> > How can I do this using Freesurfer? >>>>>>>> > > (2) If I have several subjects with labels, how can I train the >>>>>>>> > anisotropic nonstationary MRF prior as equation >>>>>>>> > (9) in the same paper? Can I use that MRF prior elsewhere in my >>>>>>>> own > program? >>>>>>>> > > Many thanks! >>>>>>>> > > Best, >>>>>>>> > Zhennan >>>>>>>> > > >>>>>>>> >>>>>>>> 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. >>>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>> >>>>> >>>>> >>> >>> >>> > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
