Thanks, Anastasia, That worked. Sorry I missed it!! --Mat -----Original Message----- From: Anastasia Yendiki [mailto:[email protected]] Sent: Monday, July 15, 2013 3:17 PM To: Hoptman, Matthew Cc: [email protected] Subject: RE: [Freesurfer] application of mri_cvs_register question
Hi Matt - Try anatorig2diff.bbr.dat. a.y On Mon, 15 Jul 2013, Hoptman, Matthew wrote: > Hi Anastasia, > Here it is: > anat2anatorig.dat anatorig2diff.bbr.dat anatorig2diff.bbr.dat.sum > diff2mni.bbr.mat > anat2anatorig.dat~ anatorig2diff.bbr.dat~ anatorig2diff.bbr.mat > mni2anat.mat > anat2anatorig.mat anatorig2diff.bbr.dat.log anatorig2mni.mat > mni2anatorig.mat > anat2diff.bbr.mat anatorig2diff.bbr.dat.log.old cvs > mni2diff.bbr.mat > anat2mni.mat anatorig2diff.bbr.dat.mincost diff2anat.bbr.mat > anatorig2anat.mat anatorig2diff.bbr.dat.param diff2anatorig.bbr.mat > > -----Original Message----- > From: Anastasia Yendiki [mailto:[email protected]] > Sent: Monday, July 15, 2013 2:56 PM > To: Hoptman, Matthew > Cc: [email protected] > Subject: RE: [Freesurfer] application of mri_cvs_register question > > > Got it. Can you send me a listing of the contents of the xfms/ directory? > Conversions b/w formats can be done with tkregister2, but the .dat file > should normally be there since it's the default format for bbregister. > > On Mon, 15 Jul 2013, Hoptman, Matthew wrote: > >> Right, that's been my problem :( Maybe something went wrong, but I didn't >> see any problem in the log files. Actually, the command I showed below had >> a typo (I used --mat rather than --reg to get that error). Is there a way >> to convert *.mat to *.dat? >> >> -----Original Message----- >> From: Anastasia Yendiki [mailto:[email protected]] >> Sent: Monday, July 15, 2013 2:44 PM >> To: Hoptman, Matthew >> Cc: [email protected] >> Subject: RE: [Freesurfer] application of mri_cvs_register question >> >> >> Hi Matt - The --reg option expects a .dat file. There should be one >> produced by bbregister in the xfms/ directory? >> >> a.y >> >> On Mon, 15 Jul 2013, Hoptman, Matthew wrote: >> >>> Hi Anastasia, >>> Yes, that was my problem. I think I need to use >>> mri_vol2vol --targ ../../../cvs_avg35_inMNI152/mri/norm.mgz --m3z >>> ../../cvs/cvs_avg35_inMNI152/final_CVSmorph_tocvs_avg35_inMNI152.m3z >>> --noDefM3zPath --reg diff2anat.bbr.mat --mov ../dtifit_FA.nii.gz --o >>> diffvol2CVS.nii.gz --no-save-reg >>> >>> >>> I now get: >>> Using the m3z file as it is; no assumed location. >>> regio_read_register(): Success >>> Error reading R[3][0] from diff2anat.bbr.mat >>> >>> Matrix from regfile: >>> -0.001 0.972 -0.234 -3.311; >>> -0.001 0.234 0.972 69.949; >>> 0.000 0.000 0.000 1.000; >>> 0.000 0.000 0.000 0.000; >>> >>> I was stuck at that point. Lilla Zollei told me she'd look into it, but >>> maybe you've communicated with her? >>> Thanks >>> Matt >>> >>> -----Original Message----- >>> From: Anastasia Yendiki [mailto:[email protected]] >>> Sent: Monday, July 15, 2013 2:30 PM >>> To: Hoptman, Matthew >>> Cc: [email protected] >>> Subject: RE: [Freesurfer] application of mri_cvs_register question >>> >>> >>> Hi Matt - The CVS morph under xfms/cvs/ maps the individual anatomical to >>> the CVS template. To map from individual diffusion to the CVS template, >>> you'd have to first use diffusion-to-anatomical affine transform file >>> under xfms/. >>> >>> Hope this helps, >>> a.y >>> >>> On Mon, 15 Jul 2013, Hoptman, Matthew wrote: >>> >>>> Hi Anastasia, >>>> Not really, what I now have is: >>>> <subject>/dmri/xfms/cvs >>>> Within cvs, there are anatomical files that are registered to the CVS >>>> template, as below, but what I DON'T have is the application of these >>>> transforms to the DTI data. That's what I'm trying to puzzle out. >>>> >>>> The files in <subject>/dmri/xfms/cvs are: >>>> c159001_to_cvs_avg35_inMNI152.mri_cvs_register.1307051306.log >>>> c159001_to_cvs_avg35_inMNI152.mri_cvs_register.1307051310.log >>>> final_CVSmorphed_tocvs_avg35_inMNI152_aseg.mgz >>>> final_CVSmorphed_tocvs_avg35_inMNI152_norm.mgz >>>> final_CVSmorph_tocvs_avg35_inMNI152.m3z >>>> lh.dbg_surf.pial >>>> lh.dbg_surf.white >>>> lh.resample.aparc.annot >>>> lh.resample.pial >>>> lh.resample.white >>>> nlalign-afteraseg-norm.mgz >>>> nlalign-aseg.mgz >>>> rh.dbg_surf.pial >>>> rh.dbg_surf.white >>>> rh.resample.aparc.annot >>>> rh.resample.pial >>>> rh.resample.white >>>> summary.c159001_to_cvs_avg35_inMNI152.mri_cvs_register.1307051306.log >>>> summary.c159001_to_cvs_avg35_inMNI152.mri_cvs_register.1307051310.log >>>> transform.txt >>>> >>>> >>>> -----Original Message----- >>>> From: Anastasia Yendiki [mailto:[email protected]] >>>> Sent: Monday, July 15, 2013 12:19 PM >>>> To: Hoptman, Matthew >>>> Cc: [email protected] >>>> Subject: Re: [Freesurfer] application of mri_cvs_register question >>>> >>>> >>>> Hi Matt - For how to tell tracula to use CVS registration, see "Specify >>>> the inter-subject registration method" here: >>>> http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula >>>> >>>> Does this answer your question? >>>> >>>> a.y >>>> >>>> On Mon, 8 Jul 2013, Hoptman, Matthew wrote: >>>> >>>>> >>>>> Hi all, >>>>> >>>>> I see how to apply mri_vol2vol to DTI data from dt_recon, but I’m not >>>>> clear on how to do so to DTI data processed in Tracula. The command in >>>>> the “Multimodal >>>>> integration and inter-subject registration” tutorial is: >>>>> >>>>> mri_vol2vol --targ templateid --m3z morph.m3z --noDefM3zPath --reg >>>>> 2anat.register.dat --mov diffvol --o diffvol2CVS --no-save-reg >>>>> >>>>> >>>>> >>>>> But in Tracula, there are no “register.dat” files, or indeed no *.dat >>>>> files. Is there a way to convert one of the *.mat files in the dmri/xfms >>>>> directory to a >>>>> *.dat file? Also, given that I think Tracula and dt_recon use different >>>>> transformation algorithms, which Tracula transform should I choose? >>>>> >>>>> >>>>> >>>>> Thanks, >>>>> >>>>> Matt >>>>> >>>>> >>>>> >>>>> Matthew J. Hoptman, PhD >>>>> Research Scientist V >>>>> Nathan S. Kline Institute for Psychiatric Research >>>>> >>>>> Research Associate Professor in Psychiatry >>>>> NYU School of Medicine >>>>> >>>>> >>>>> >>>>> IMPORTANT NOTICE: This e-mail is meant only for the use of the intended >>>>> recipient. 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