Freesurfer January 2012

freesurfer@nmr.mgh.harvard.edu

97 participants
171 discussions

dividing a label into equal parts
by Ritobrato Datta 18 Jan '12

18 Jan '12

Is there a way to divide a surface label like V1 into equal parts (say 10 parts) either along its length or width and save each part as a separate label ? Drawing them in tkmedit is quite crude and not very accurate. Please let me know. Thanks Ri

3 2

Re: [Freesurfer] Thanks so much!
by Lilla Zollei 18 Jan '12

18 Jan '12

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 <lzollei(a)nmr.mgh.harvard.edu> > To: Antonella Kis <atorok9(a)yahoo.com> > Cc: freesurfer(a)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 <lzollei(a)nmr.mgh.harvard.edu> > > To: Antonella Kis <atorok9(a)yahoo.com> > > Cc: freesurfer(a)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 <lzollei(a)nmr.mgh.harvard.edu> > > > To: Antonella Kis <atorok9(a)yahoo.com> > > > Cc: freesurfer(a)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(a)nmr.mgh.harvard.edu> > > > > To: Antonella Kis <atorok9(a)yahoo.com> > > > > Cc: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)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(a)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(a)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. > > > >

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Re: [Freesurfer] THANKS
by Lilla Zollei 18 Jan '12

18 Jan '12

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 <lzollei(a)nmr.mgh.harvard.edu> > To: Antonella Kis <atorok9(a)yahoo.com> > Cc: freesurfer(a)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 <lzollei(a)nmr.mgh.harvard.edu> > > To: Antonella Kis <atorok9(a)yahoo.com> > > Cc: freesurfer(a)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(a)nmr.mgh.harvard.edu> > > > To: Antonella Kis <atorok9(a)yahoo.com> > > > Cc: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)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(a)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. > > > >

1 0

Re: [Freesurfer] How to define the FA-mask
by Lilla Zollei 18 Jan '12

18 Jan '12

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(a)nmr.mgh.harvard.edu> > To: Antonella Kis <atorok9(a)yahoo.com> > Cc: freesurfer(a)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(a)nmr.mgh.harvard.edu> > > To: Antonella Kis <atorok9(a)yahoo.com> > > Cc: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)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. > > > > > > > > > > >

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Re: [Freesurfer] How to define the FA-mask
by Lilla Zollei 18 Jan '12

18 Jan '12

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(a)nmr.mgh.harvard.edu> > To: Antonella Kis <atorok9(a)yahoo.com> > Cc: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)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. > > > >

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How to define the FA-mask
by Antonella Kis 18 Jan '12

18 Jan '12

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

2 1

Cortical thickness information
by Rashmi Singh 18 Jan '12

18 Jan '12

Hey Bruce, Thank you for the informations. May I ask you few additional questions? A) In your answer to my first question you wrote "you can also just look at the map itself without averaging over an ROI". What does this mean in reference to calculation of the cortical thickness. B) For my question B in my previous e mail, may be I was not clear, I am actually asking you about the information present in the ?.aparc .stats file that is not in the table. As I understand the table represents the different ROI and has information of the mean (average) thickness within each ROI of the cortical parcellation ( 35 different regions). But there are some additional information present before the table begins. And it says # Measure Cortex,NumVert,Number of Vertices, 143103, unitless # Measure Cortex, WhiteSurfArea, White Surface Total Area, 94823.1, mm^2 # Measure Cortex, MeanThickness,Mean Thickness, 2.62665, mm My question is about this measurement. What does this Cortical measure mean thickness is representing? C) Can you please explain me a little bit in detain how would I run the mris_anatomical_stats, I mean can you help me with the command line or suggest me a tutorial where I can find the information? D) I don't know what is qdec? Please advise. E) If I want to know the total cortical surface area do I add up the surface area measurements for each ROI given in the table for each hemisphere and then I add the two individual hemisphere measurements for getting the total cortical surface area? Looking forward for your response, Thanks, Rashmi. " On 1/18/12 9:18 AM, "Bruce Fischl" <fischl(a)nmr.mgh.harvard.edu<mailto:fischl@nmr.mgh.harvard.edu>> wrote: On Wed, 18 Jan 2012, Rashmi Singh wrote: Hello, This is Rashmi. I am very new to neurobiology and computing and my very first project involves measuring cortical thickness from the reconstructed surfaces generated by FreeSurfer. I have recently started to self teach myself FreeSurfer, but with a background in immunology and almost no background in neurobiology I know I have a long way to go and need a lot of help. I have learnt to run FreeSurfer and am currently using Version 5.1.0. I am also referring the FreeSurfer Lectures and Tutorial available online for free to learn usage of Tktools. Despite that I don't have access to your tutorial data, I have found this tutorial helpful in learning how to use Tktools to view volumes and surfaces. At present I have few basic (naïve) questions that I need your help with, excuse me if you find my question ignorant. A)My first question is about the cortical parcellation stats files. After running the recon all on my MPRAGE data, I did get the ?.aparc.stats file in the stats folder. I also see ?.aparc.a2009S.stats files. I read and kind of understood the difference between these two files in how differently they calculate the gray matter. My question is which of these two files should be considered for measurement as generated by the automated calculation of the cortical thickness. the thickness is a map over the whole cortex. The aparc and aparc.a2009S are different regions of interest (ROIs) that follow different anatomical conventions. You can use either to obtain the average thickness in the ROIs contained in each, but you can also just look at the map itself without averaging over an ROI. B) Besides the cortical thickness parameters the ?.aparc file has information on the white surface area and the mean thickness. Is the mean thickens represents the average cortical thickness of the respective hemisphere? If not what does it represents and how can I calculate the hemisphere based cortical thickness? the mean thickness is the mean within each ROI. mris_anatomical_stats will compute the mean thickness over the hemi if you want. C) How would I calculate the average cortical thickness of the whole brain? average the two hemi thicknesses. That will be close enough D) In research articles related to measurement of cortical thickness, authors have reported mapping of the thickness measured on the inflated or semi-inflated surface . How is it done and what is the significance of doing it. this is for visualization. Just bring up the inflated surface in tksurfer and load the lh or rh thickness. E)Once I have the measure of all the cortical thickness how do I compare all the Subjects measurements participating in my study? qdec is probably the easiest way to do this. F) Do you in your tutorial have some reference images for labelled subcortical regions that are generated in aseg.mgz files. yes, we use an atlas that we compiled from manually labeled subjects here at MGH. Thanks for your response in advance. Hope to hear from you soon. Regards, Rashm. _________________________________________________________________________ ___ This document may contain information covered under the Privacy Act, 5 USC 552(a), and/or the Health Insurance Portability and Accountability Act (PL 104-191) and its various implementing regulations and must be protected in accordance with those provisions. Healthcare information is personal and sensitive and must be treated accordingly. If this correspondence contains healthcare information it is being provided to you after appropriate authorization from the patient or under circumstances that don't require patient authorization. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Redisclosure without additional patient consent or as permitted by law is prohibited. Unauthorized redisclosure or failure to maintain confidentiality subjects you to application of appropriate sanction. If you have received this correspondence in error, please notify the sender at once and destroy any copies you have made. 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. ________________________________ This document may contain information covered under the Privacy Act, 5 USC 552(a), and/or the Health Insurance Portability and Accountability Act (PL 104-191) and its various implementing regulations and must be protected in accordance with those provisions. Healthcare information is personal and sensitive and must be treated accordingly. If this correspondence contains healthcare information it is being provided to you after appropriate authorization from the patient or under circumstances that don't require patient authorization. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Redisclosure without additional patient consent or as permitted by law is prohibited. Unauthorized redisclosure or failure to maintain confidentiality subjects you to application of appropriate sanction. If you have received this correspondence in error, please notify the sender at once and destroy any copies you have made.

1 0

Freesurfer flips brains?
by Léoné, F.T.M. (Frank) 18 Jan '12

18 Jan '12

Dear all, I must be missing something really obvious, but it seems my brains are flipped. What I do: - I have a highres structural scan, nii file format - I convert it to a surface using recon-all - Coregister the highres structural to the functional scan, so it is in the voxel size and orientation as the functional scans - I try to bbregister the coregistered and resliced T1 with the surface But then: hey, it doesn't fit, my low-res T1 is flipped compared to my y surface, hence to my original T1. So is it indeed true that my T1 might have been flipped? If so, does it make a wrong assumption on neurological vs radiological convention, or what is going on? Thanks in advance, best, Frank

2 1

Re: [Freesurfer] rendering problem
by Gabriel Gonzalez Escamilla 18 Jan '12

18 Jan '12

3 2

Cortical thickness question
by Rashmi Singh 18 Jan '12

18 Jan '12

Hello, This is Rashmi. I am very new to neurobiology and computing and my very first project involves measuring cortical thickness from the reconstructed surfaces generated by FreeSurfer. I have recently started to self teach myself FreeSurfer, but with a background in immunology and almost no background in neurobiology I know I have a long way to go and need a lot of help. I have learnt to run FreeSurfer and am currently using Version 5.1.0. I am also referring the FreeSurfer Lectures and Tutorial available online for free to learn usage of Tktools. Despite that I don't have access to your tutorial data, I have found this tutorial helpful in learning how to use Tktools to view volumes and surfaces. At present I have few basic (naïve) questions that I need your help with, excuse me if you find my question ignorant. A)My first question is about the cortical parcellation stats files. After running the recon all on my MPRAGE data, I did get the ?.aparc.stats file in the stats folder. I also see ?.aparc.a2009S.stats files. I read and kind of understood the difference between these two files in how differently they calculate the gray matter. My question is which of these two files should be considered for measurement as generated by the automated calculation of the cortical thickness. B) Besides the cortical thickness parameters the ?.aparc file has information on the white surface area and the mean thickness. Is the mean thickens represents the average cortical thickness of the respective hemisphere? If not what does it represents and how can I calculate the hemisphere based cortical thickness? C) How would I calculate the average cortical thickness of the whole brain? D) In research articles related to measurement of cortical thickness, authors have reported mapping of the thickness measured on the inflated or semi-inflated surface . How is it done and what is the significance of doing it. E)Once I have the measure of all the cortical thickness how do I compare all the Subjects measurements participating in my study? F) Do you in your tutorial have some reference images for labelled subcortical regions that are generated in aseg.mgz files. Thanks for your response in advance. Hope to hear from you soon. Regards, Rashm. ________________________________ This document may contain information covered under the Privacy Act, 5 USC 552(a), and/or the Health Insurance Portability and Accountability Act (PL 104-191) and its various implementing regulations and must be protected in accordance with those provisions. Healthcare information is personal and sensitive and must be treated accordingly. If this correspondence contains healthcare information it is being provided to you after appropriate authorization from the patient or under circumstances that don't require patient authorization. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Redisclosure without additional patient consent or as permitted by law is prohibited. Unauthorized redisclosure or failure to maintain confidentiality subjects you to application of appropriate sanction. If you have received this correspondence in error, please notify the sender at once and destroy any copies you have made.

2 1

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Freesurfer January 2012