What directory are you in? Is your registration file (diff2anat.bbr.mat)
in the same directory as where you are calling the command from?
Lilla
On Wed, 10 Jul 2013, Hoptman, Matthew wrote:
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:[email protected]]
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:[email protected]]
Sent: Tuesday, July 09, 2013 8:01 PM
To: Hoptman, Matthew
Cc: [email protected]
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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