Dear all,
On the FS Tutorial/Diffusion the FA masked is defined as:
mri_mask $TUTORIAL_DIR/$subj/dtrecon/fa.nii \
$SUBJECTS_DIR/$subj/mri/wmparc2diff.mgz \
$TUTORIAL_DIR/$subj/dtrecon/fa-masked.mgzand when it follows the resampling on
the CVS space I see:
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-regwith the following explanation: The '--interp'
flag indicates the type of interpolation we want to use
for our resampling. We are not using a segmented volume as an input so
we use the default trilinear (trilin) interpolation option. If you
wanted to resample a segmentation volume (such as wmparc or aseg) in
CVS space, you would want to use the nearest neighbor (nearest)
interpolation option.
I don't understand what exactly means: "We are not using a segmented volume as
an input" since the fa-masked is defined using the wmparc2diff?
I understood there two masking options: (option 1) using the wmparc to guide
my masking or (option 2) if I want to
do the masking based upon intensity values found in the fa image.
I am not sure how will be the best to define my FA-mask if I was running the
CVS registration with the option --noaseg and also I want to do a group study
and see if my Fa values increases or decreases in controls vs. patients. Can
you please give me an advise?
Also, I am not sure if I am mixing things or not but can I define my mask
using the wmparc if I did the registration with the --noaseg option?
Many thanks.
Antonella_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
