Yes, but then you would not use --reg $TUTORIAL_DIR/$subj/dtrecon/register.dat
with mri_vol2vol.
--Lilla On Wed, 18 Jan 2012, Antonella Kis wrote:
Finally I understood! THANKS so much Lilla! So I can use the nearst interp if while resampling in the CVS space my input (--mov) volume is replaced from --mov $TUTORIAL_DIR/$subj/dtrecon/fa-masked.mgz \ with for example /media/2Tra/Antonella_2011/DTI_FS/dtrecon_cvs/P04_cvs/P04/mri/wmparc.mgz? THANKS SO MUCH! Antonella ___________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________ From: Lilla Zollei <lzol...@nmr.mgh.harvard.edu> To: Antonella Kis <ator...@yahoo.com> Cc: freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, January 18, 2012 4:02 PM Subject: Re: [Freesurfer] THANKS Yes, that is right. On Wed, 18 Jan 2012, Antonella Kis wrote: > Thanks so much now I more clear. So based on my understanding when resampling on CVS space we will use the nears interpolation if instead of the fa-masked.mgz we have a segmentation volume such as wmparc.mgz or the aparc+aseg.mgz but if I have fa-masked.mgz no matter > how I defined my mask I will have use the --interp trilin while resampling since the fa-masked.mgz is not a segmentation file. > > Is this right? > > Sorry for asking so many silly questions. > > Thanks. > Antonella > >__________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________ _ > From: Lilla Zollei <lzol...@nmr.mgh.harvard.edu> > To: Antonella Kis <ator...@yahoo.com> > Cc: freesurfer@nmr.mgh.harvard.edu > Sent: Wednesday, January 18, 2012 3:46 PM > Subject: Re: [Freesurfer] How to define the FA-mask > > > 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 <lzol...@nmr.mgh.harvard.edu> > > To: Antonella Kis <ator...@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 <lzol...@nmr.mgh.harvard.edu> > > > To: Antonella Kis <ator...@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 > > > > > > > > > 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. > > > > > > > > > > > > > > > > > > > _______________________________________________ > 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. > > > > _______________________________________________ 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.
_______________________________________________ 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.
