Re: [Freesurfer] Repost: Make liberal ROI masks
You'll need to merge the WM parcellation labels with those of their
matching GM parcellations. We do not have explicit software to do this.
You can do it in matlab, something like
a = MRIread('aparc.a2009s+aseg_liberal.mgz);
ind = find(a.vol == 3030); % 3030 = wm-lh-superiortemporal from
FreeSurferColorLUT.txt
a.vol(ind) = 1030; % 1030 = ctx-lh-superiortemporal
Do the rest of the parcellations in the same way, then
MRIwrite(a,'aparc.a2009s+aseg_liberal2.mgz');
On 08/10/2015 01:29 PM, Martin Hebart wrote:
Dear all,
In an earlier post, I was asking for help implementing dilated ROIs.
I was using Doug's suggestion
mri_aparc2aseg --subject 01 --a2009s --labelwm --wmparc-dmax 2 --o
aparc.a2009s+aseg_liberal.mgz
followed by
mri_label2vol --seg aparc.a2009s+aseg_liberal.mgz --regheader orig.mgz
--o rois.nii --temp sub.nii --subject 01
However, the written images are very similar to the original undilated
ROIs, so I guess this has to do with the fact that they labels within
white matter are still classified as white matter.
My question: How can I write the ROIs from the dilated labels?
Thanks!
Martin
P.S.: If this all is very difficult or impossible, I would be happy if
I could just write out a nifti for each label in the annotation file
which for each voxel reflects the probability of that label (i.e. not
binary masks, but probabilistic masks). Then I could do this process
manually.
2015-07-15 18:10 GMT+02:00 Martin Hebart martin.heb...@gmail.com
mailto:martin.heb...@gmail.com:
Dear Thomas and Doug,
Thanks a lot for your replies, I believe you fully answered my
question.
@Thomas: The reason I would like to dilate masks into white matter
is that although the masks are quite accurate for structural
volumes, the functional data doesn't perfectly fit the structural
(even when using a fieldmap). I don't want to miss any grey matter
voxels that might carry information, while including some white
matter is - for the purpose of my task - not detrimental.
Thanks again, I will try to implement Doug's suggestion!
Martin
2015-07-15 15:12 GMT+02:00 Thomas Yeo ytho...@csail.mit.edu
mailto:ytho...@csail.mit.edu:
Hi Martin,
I am a little confused. Can you explain a little more about
what you
need? Do you want the freesurfer cortical ROIs dilated into the
surrounding regions like white matter and CSF or something? If so,
then Doug's suggestion sounds reasonable.
In the case of my parcellation, I ran the MNI152 template through
recon-all, which unfortunately resulted in an overly conservative
estimate of gray matter (i.e., the tight mask in
https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation_Yeo2011).
Therefore I went through a rather complicated way of
generating the
liberal mask by registering the recon-all of 1000 subjects to MNI
space.
Since you appear to be working on an individual subject, the
freesurfer estimate of the cortical ROIs is likely to be quite
accurate. Why might you want to dilate them into CSF or white
matter?
Regards,
Thomas
On Wed, Jul 15, 2015 at 12:38 AM, Douglas N Greve
gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu
wrote:
There is not an easy way to do that, though Thomas might
want to chime
in. I would probably use the code that generates the wmparc
(mri_aparc2aseg --labelwm) to create labels in the adjacent
WM out to a
few mm (--wmparc-dmax 2), then merge the WM labels with the
GM labels
On 07/14/2015 08:18 AM, Martin Hebart wrote:
Dear Freesurfer users,
I would be really happy if someone could help me out on the
issue I
mentioned below.
What I want to do is create non-overlapping anatomical ROI
masks that
are not restricted to grey matter only.
Thanks a lot in advance!
Martin
-
Dear all,
I've created non-overlapping ROI masks using
mri_label2vol --seg aparc.a2009s+aseg.mgz --regheader
orig.mgz --o
rois.nii --temp sub.nii --subject 01
Now these ROI masks are actually quite conservative
concerning grey
matter vs. other structures, i.e. they are only on the grey
matter.
I've seen more liberal masks e.g. here:
https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation_Yeo2011
I would like to create similarly liberal non-overlapping
ROI masks for
all ROIs in the voxel size defined by the image in --temp, but
Re: [Freesurfer] Repost: Make liberal ROI masks
Dear all, In an earlier post, I was asking for help implementing dilated ROIs. I was using Doug's suggestion mri_aparc2aseg --subject 01 --a2009s --labelwm --wmparc-dmax 2 --o aparc.a2009s+aseg_liberal.mgz followed by mri_label2vol --seg aparc.a2009s+aseg_liberal.mgz --regheader orig.mgz --o rois.nii --temp sub.nii --subject 01 However, the written images are very similar to the original undilated ROIs, so I guess this has to do with the fact that they labels within white matter are still classified as white matter. My question: How can I write the ROIs from the dilated labels? Thanks! Martin P.S.: If this all is very difficult or impossible, I would be happy if I could just write out a nifti for each label in the annotation file which for each voxel reflects the probability of that label (i.e. not binary masks, but probabilistic masks). Then I could do this process manually. 2015-07-15 18:10 GMT+02:00 Martin Hebart martin.heb...@gmail.com: Dear Thomas and Doug, Thanks a lot for your replies, I believe you fully answered my question. @Thomas: The reason I would like to dilate masks into white matter is that although the masks are quite accurate for structural volumes, the functional data doesn't perfectly fit the structural (even when using a fieldmap). I don't want to miss any grey matter voxels that might carry information, while including some white matter is - for the purpose of my task - not detrimental. Thanks again, I will try to implement Doug's suggestion! Martin 2015-07-15 15:12 GMT+02:00 Thomas Yeo ytho...@csail.mit.edu: Hi Martin, I am a little confused. Can you explain a little more about what you need? Do you want the freesurfer cortical ROIs dilated into the surrounding regions like white matter and CSF or something? If so, then Doug's suggestion sounds reasonable. In the case of my parcellation, I ran the MNI152 template through recon-all, which unfortunately resulted in an overly conservative estimate of gray matter (i.e., the tight mask in https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation_Yeo2011). Therefore I went through a rather complicated way of generating the liberal mask by registering the recon-all of 1000 subjects to MNI space. Since you appear to be working on an individual subject, the freesurfer estimate of the cortical ROIs is likely to be quite accurate. Why might you want to dilate them into CSF or white matter? Regards, Thomas On Wed, Jul 15, 2015 at 12:38 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: There is not an easy way to do that, though Thomas might want to chime in. I would probably use the code that generates the wmparc (mri_aparc2aseg --labelwm) to create labels in the adjacent WM out to a few mm (--wmparc-dmax 2), then merge the WM labels with the GM labels On 07/14/2015 08:18 AM, Martin Hebart wrote: Dear Freesurfer users, I would be really happy if someone could help me out on the issue I mentioned below. What I want to do is create non-overlapping anatomical ROI masks that are not restricted to grey matter only. Thanks a lot in advance! Martin - Dear all, I've created non-overlapping ROI masks using mri_label2vol --seg aparc.a2009s+aseg.mgz --regheader orig.mgz --o rois.nii --temp sub.nii --subject 01 Now these ROI masks are actually quite conservative concerning grey matter vs. other structures, i.e. they are only on the grey matter. I've seen more liberal masks e.g. here: https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation_Yeo2011 I would like to create similarly liberal non-overlapping ROI masks for all ROIs in the voxel size defined by the image in --temp, but excluding specific tissue types such as white matter, CSF, and other non-grey matter tissue. What would be the best way to do so? Cheers, Martin ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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
Re: [Freesurfer] Repost: Make liberal ROI masks
Dear Thomas and Doug, Thanks a lot for your replies, I believe you fully answered my question. @Thomas: The reason I would like to dilate masks into white matter is that although the masks are quite accurate for structural volumes, the functional data doesn't perfectly fit the structural (even when using a fieldmap). I don't want to miss any grey matter voxels that might carry information, while including some white matter is - for the purpose of my task - not detrimental. Thanks again, I will try to implement Doug's suggestion! Martin 2015-07-15 15:12 GMT+02:00 Thomas Yeo ytho...@csail.mit.edu: Hi Martin, I am a little confused. Can you explain a little more about what you need? Do you want the freesurfer cortical ROIs dilated into the surrounding regions like white matter and CSF or something? If so, then Doug's suggestion sounds reasonable. In the case of my parcellation, I ran the MNI152 template through recon-all, which unfortunately resulted in an overly conservative estimate of gray matter (i.e., the tight mask in https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation_Yeo2011). Therefore I went through a rather complicated way of generating the liberal mask by registering the recon-all of 1000 subjects to MNI space. Since you appear to be working on an individual subject, the freesurfer estimate of the cortical ROIs is likely to be quite accurate. Why might you want to dilate them into CSF or white matter? Regards, Thomas On Wed, Jul 15, 2015 at 12:38 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: There is not an easy way to do that, though Thomas might want to chime in. I would probably use the code that generates the wmparc (mri_aparc2aseg --labelwm) to create labels in the adjacent WM out to a few mm (--wmparc-dmax 2), then merge the WM labels with the GM labels On 07/14/2015 08:18 AM, Martin Hebart wrote: Dear Freesurfer users, I would be really happy if someone could help me out on the issue I mentioned below. What I want to do is create non-overlapping anatomical ROI masks that are not restricted to grey matter only. Thanks a lot in advance! Martin - Dear all, I've created non-overlapping ROI masks using mri_label2vol --seg aparc.a2009s+aseg.mgz --regheader orig.mgz --o rois.nii --temp sub.nii --subject 01 Now these ROI masks are actually quite conservative concerning grey matter vs. other structures, i.e. they are only on the grey matter. I've seen more liberal masks e.g. here: https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation_Yeo2011 I would like to create similarly liberal non-overlapping ROI masks for all ROIs in the voxel size defined by the image in --temp, but excluding specific tissue types such as white matter, CSF, and other non-grey matter tissue. What would be the best way to do so? Cheers, Martin ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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.
Re: [Freesurfer] Repost: Make liberal ROI masks
Hi Martin, I am a little confused. Can you explain a little more about what you need? Do you want the freesurfer cortical ROIs dilated into the surrounding regions like white matter and CSF or something? If so, then Doug's suggestion sounds reasonable. In the case of my parcellation, I ran the MNI152 template through recon-all, which unfortunately resulted in an overly conservative estimate of gray matter (i.e., the tight mask in https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation_Yeo2011). Therefore I went through a rather complicated way of generating the liberal mask by registering the recon-all of 1000 subjects to MNI space. Since you appear to be working on an individual subject, the freesurfer estimate of the cortical ROIs is likely to be quite accurate. Why might you want to dilate them into CSF or white matter? Regards, Thomas On Wed, Jul 15, 2015 at 12:38 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: There is not an easy way to do that, though Thomas might want to chime in. I would probably use the code that generates the wmparc (mri_aparc2aseg --labelwm) to create labels in the adjacent WM out to a few mm (--wmparc-dmax 2), then merge the WM labels with the GM labels On 07/14/2015 08:18 AM, Martin Hebart wrote: Dear Freesurfer users, I would be really happy if someone could help me out on the issue I mentioned below. What I want to do is create non-overlapping anatomical ROI masks that are not restricted to grey matter only. Thanks a lot in advance! Martin - Dear all, I've created non-overlapping ROI masks using mri_label2vol --seg aparc.a2009s+aseg.mgz --regheader orig.mgz --o rois.nii --temp sub.nii --subject 01 Now these ROI masks are actually quite conservative concerning grey matter vs. other structures, i.e. they are only on the grey matter. I've seen more liberal masks e.g. here: https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation_Yeo2011 I would like to create similarly liberal non-overlapping ROI masks for all ROIs in the voxel size defined by the image in --temp, but excluding specific tissue types such as white matter, CSF, and other non-grey matter tissue. What would be the best way to do so? Cheers, Martin ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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
[Freesurfer] Repost: Make liberal ROI masks
Dear Freesurfer users, I would be really happy if someone could help me out on the issue I mentioned below. What I want to do is create non-overlapping anatomical ROI masks that are not restricted to grey matter only. Thanks a lot in advance! Martin - Dear all, I've created non-overlapping ROI masks using mri_label2vol --seg aparc.a2009s+aseg.mgz --regheader orig.mgz --o rois.nii --temp sub.nii --subject 01 Now these ROI masks are actually quite conservative concerning grey matter vs. other structures, i.e. they are only on the grey matter. I've seen more liberal masks e.g. here: https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation_Yeo2011 I would like to create similarly liberal non-overlapping ROI masks for all ROIs in the voxel size defined by the image in --temp, but excluding specific tissue types such as white matter, CSF, and other non-grey matter tissue. What would be the best way to do so? Cheers, Martin ___ 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.
Re: [Freesurfer] Repost: Make liberal ROI masks
There is not an easy way to do that, though Thomas might want to chime in. I would probably use the code that generates the wmparc (mri_aparc2aseg --labelwm) to create labels in the adjacent WM out to a few mm (--wmparc-dmax 2), then merge the WM labels with the GM labels On 07/14/2015 08:18 AM, Martin Hebart wrote: Dear Freesurfer users, I would be really happy if someone could help me out on the issue I mentioned below. What I want to do is create non-overlapping anatomical ROI masks that are not restricted to grey matter only. Thanks a lot in advance! Martin - Dear all, I've created non-overlapping ROI masks using mri_label2vol --seg aparc.a2009s+aseg.mgz --regheader orig.mgz --o rois.nii --temp sub.nii --subject 01 Now these ROI masks are actually quite conservative concerning grey matter vs. other structures, i.e. they are only on the grey matter. I've seen more liberal masks e.g. here: https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation_Yeo2011 I would like to create similarly liberal non-overlapping ROI masks for all ROIs in the voxel size defined by the image in --temp, but excluding specific tissue types such as white matter, CSF, and other non-grey matter tissue. What would be the best way to do so? Cheers, Martin ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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.
