fa-masked is a masked volume and not a segmentation file. A segmentation file contains labels that correspond to certain anatomical areas. The fa-masked file is the same as your fa volume but some background regions are eliminated from it using the mask volume.
On Wed, 18 Jan 2012, Antonella Kis wrote:
Thank you Lilla, this is very helpful. Just one more question please: why it says it is not a segmented volume the input volume which in fact you mentioned is the fa-masked.mgz if this was defined using the wmparc?
THANKS and have a great day! Antonella
From: Lilla Zollei lzollei@nmr.mgh.harvard.edu To: Antonella Kis atorok9@yahoo.com Cc: freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, January 18, 2012 3:38 PM Subject: Re: [Freesurfer] How to define the FA-mask
Hi,
Many thanks for your reply. Can ypu please advise me how I should calculate the mask if I want to do the masking based upon intensity values found in the fa image?
I tried to run (without wmparc) but it gave me error:
mri_mask $TUTORIAL_DIR/$subj/dtrecon/fa.nii \ $TUTORIAL_DIR/$subj/dtrecon/fa-masked.mgz
Sorry, you should use mri_threshold if you want to do intensity thresholding and mri_mask if you want to use a mask. In the above the second argument, the mask, is missing.
On the tutorial site which is the input volume that it says is not a segmented volume during resampling on the CVS:
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
It is "$TUTORIAL_DIR/$subj/dtrecon/fa-masked.mgz"
Based on your experience What will be the best to use when I define my voxels the parcellation map or an intensity threshol?
It really depends on your data. You might want to look at both outputs on a couple of data sets and then decide.
--Lilla
From: Lilla Zollei lzollei@nmr.mgh.harvard.edu To: Antonella Kis atorok9@yahoo.com Cc: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, January 18, 2012 2:34 PM Subject: Re: [Freesurfer] How to define the FA-mask
mri_mask $TUTORIAL_DIR/$subj/dtrecon/fa.nii \ $SUBJECTS_DIR/$subj/mri/wmparc2diff.mgz \ $TUTORIAL_DIR/$subj/dtrecon/fa-masked.mgz and 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-reg with 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?
When you masked the FA volume, you eliminated some values that are outside of the mask but did not create a binary volume, the original FA values remained in the volume.
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?
These two things are not related. When considering the masking the only thing you need to think about is whethe ryou trust the parcellation map or an intensity threshold better in order to define voxels that you would like to keep in your input volume.
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?
Again, these deceisions are not related.
Lilla
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