Hi Lilla, Unfortunately, when I run: 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;
Best, Matt -----Original Message----- From: Lilla Zollei [mailto:lzollei@nmr.mgh.harvard.edu] Sent: Wednesday, July 10, 2013 6:07 PM To: Hoptman, Matthew Subject: RE: [Freesurfer] application of mri_cvs_register question
Hi Matt,
As diff2anat.bbr.mat was created by bbregister, I believe you should be able to use --reg diff2anat.bbr.mat in your command.
Let me know if you encounter further problems.
Lilla
On Wed, 10 Jul 2013, Hoptman, Matthew wrote:
Hi Lilla, I want to apply the transform to both the dtifit_FA and tracula tracts to put them into cvs space (given the m3z file, as well). The goal is to get "average" tracts across my subjects. The relevant transforms I have in my dmri/xfms would seem to be: diff2anat.bbr.mat diff2anatorig.bbr.mat diff2mni.bbr.mat
Thanks, Matt -----Original Message----- From: Lilla Zollei [mailto:lzollei@nmr.mgh.harvard.edu] Sent: Tuesday, July 09, 2013 8:01 PM To: Hoptman, Matthew Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] application of mri_cvs_register question
Hi,
What type of registration file do you have representing the diff2anat transformation? With mri_vol2vol you can use many different types of transformations, if you switch the --reg flag to --xfm, --fsl or --lta, for example.
Lilla
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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