Hi Antonella,
1) Can you please help me find or get the the cvs_avg35/mri/norm.mgz? I saw
online the same question was posted on June 2011 but there is no answer for the
question online:
http://www.opensubscriber.com/message/freesurfer@nmr.mgh.harvard.edu/15506607.html
Have you run the cvs_registration code? If you have, then you have to have
the template. If you have not, I can make the template subject available
for you for download.
2) Since for my TBSS TBSS study was used by the TBSS the nonlinear
registration FNIRT (is about 15 times faster than IRTK on FA data and possibly
a little more 'accurate') I would like to use for a Tal space a non-linear
talairach registration. Can you please give
me some directions on how I can do this? What is the default Tal registration
(linear or non-linear) for dt_recon?
dt_recon produces a linear registration to the Tal space. If you have
ran recon-all on your structural data you should also have access to
talairach.m3z that aligns your subject in the fsaverage space.
3) When dt_recon is aligning the diffusion data in the Tal space is in fact
aligning the register.dat data (difussion data already aligned to the
structural data) and the output is the fa-tal.nii.gz? If not why I need the
register.dat file?
I don't understand your question, but
* register.dat is the registrationfile that encodes the transform going
from the diffusion to the structural space. If you want to resample any of
your diffusion related files in the structural space you will need to use
mri_vol2vol and that file to do so.
* fa-tal.nii.gz is a completely different file. It is the fa volume that
got resampled in the Tal space using a linear transformation
(talairach.xfm via the structural data).
4) So by my understanding each subject will have a file called fa-tal.nii which
in fact represents the subject's registration on the Tal-space? How about the
mean diffusivity? I don't have only one file for this adc.nii. What if I want
to do a non_FA values study on
the tal space?
You need to run the follwoing command, replacing fa with the scalar volume
of your interest.
set reg = register.dat
set fa = fa.nii
set fatal = fa-tal.nii.gz
set cmd = (mri_vol2vol --reg $reg --tal --mov $fa --o $fatal)
5) I understood that the 'registration.dat' file describes a rigid-body
transformation from the diffusion to the structural space and in order to
resample the structural volume in the diffusion space, I will need to apply the
inverse of this transformation to my
input volumes and to use for this the 'mri_vol2vol':
mri_vol2vol --mov $TUTORIAL_DIR/$subj/dtrecon/lowb.nii \
--targ $SUBJECTS_DIR/$subj/mri/wmparc.mgz \
--inv --interp nearest --o $SUBJECTS_DIR/$subj/mri/wmparc2diff.mgz \
--reg $TUTORIAL_DIR/$subj/dtrecon/register.dat --no-save-reg
Is the register.dat file created by this function mri_vol2vol? I believe the
registration between the diffusion and structural space (so the register.dat
file) has already
been computed as part of the previous pre-processing step so while using the
mri_vol2vol as above do I need to use the '--no-save-reg' flag as in the above
example or the '--save-reg' flag?
register.dat gets created using dt_recon and mri_vol2vol just applies that
transform. --no-save-reg just tells the command not to save a copy of the
inverse transform that gets applied.
6) To resample the diffusion data of one subject in the CVS space do I need to
run after dt_recon the mri_vol2vol as below?
mri_vol2vol --targ
$FREESURFER_HOME/subjects/cvs_avg35/mri/norm.mgz \
--m3z
$SUBJECTS_DIR/$subj/cvs/combined_tocvs_avg35_elreg_afteraseg-norm.m3z \
--noDefM3zPath --reg $TUTORIAL_DIR/$subj/dtrecon/register.dat \
--mov $TUTORIAL_DIR/$subj/dtrecon/fa-masked.mgz \
--o $TUTORIAL_DIR/$subj/dtrecon/fa-masked.ANAT+CVS-to-avg35.mgz \
--interp trilin --no-save-reg
Do I need to run the mri_cvs_registration on the structural data in order to
get the above .m3z file 'combined_tocvs_avg35_elreg_afteraseg-norm.m3z' before
I run the mri_vol2vol?
If I want to have my second registration step done in the Tal space not CVS
space since after running dt_recon I am getting the fa-tal.nii.gz and the
fa-masked.mgz
is this the equivalent file to fa-masked.ANAT+CVS-to-avg35.mgz (if I use the
CVS space)? In this case I don't need to run the last mri_vol2vol command?
Sorry for asking so many questions but it is very confusing the online material.
Yes, you will run mri_cvs_register on the structural data and that will
compute your m3z file.
fa-masked is in the native diffusion space and fa-tal is in the Talairach
space so they are not equivalent with each other, they don't live in the
same space.
--Lilla
From: Lilla Zollei lzol...@nmr.mgh.harvard.edu
To: Antonella Kis ator...@yahoo.com
Cc: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu
Sent:
