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:ayend...@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:ayend...@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:ayend...@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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