Thanks, Anastasia, That worked. Sorry I missed it!! --Mat
-----Original Message----- From: Anastasia Yendiki [mailto:ayendiki@nmr.mgh.harvard.edu] Sent: Monday, July 15, 2013 3:17 PM To: Hoptman, Matthew Cc: freesurfer@nmr.mgh.harvard.edu 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:ayendiki@nmr.mgh.harvard.edu] Sent: Monday, July 15, 2013 2:56 PM To: Hoptman, Matthew Cc: freesurfer@nmr.mgh.harvard.edu 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:ayendiki@nmr.mgh.harvard.edu] Sent: Monday, July 15, 2013 2:44 PM To: Hoptman, Matthew Cc: freesurfer@nmr.mgh.harvard.edu 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:ayendiki@nmr.mgh.harvard.edu] Sent: Monday, July 15, 2013 2:30 PM To: Hoptman, Matthew Cc: freesurfer@nmr.mgh.harvard.edu 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:ayendiki@nmr.mgh.harvard.edu] Sent: Monday, July 15, 2013 12:19 PM To: Hoptman, Matthew Cc: freesurfer@nmr.mgh.harvard.edu 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
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