Dear group, I'm trying to morph the Buckner2011http://www.freesurfer.net/fswiki/CerebellumParcellation_Buckner2011 cerebellum segmentation map from MNI152 to subject's space: mri_vol2vol --mov subjects/sub01/mri/norm.mgz --s sub01 --targ Buckner2011_17Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz --m3z talairach.m3z --o sub01_Buckner2011_atlas_17_loose.nii.gz --nearest --inv-morph It worked with the 17 networks, but didn't work with the 7 networks version. Any ideas? This is really strange.
Thanks, Noam
Hi Noam,
This should be a two step procedure, rather than a one-step procedure. Here's a previous email I sent to the list about warping Choi's striatum atlas to individual subject's striatum (which I have modified for the cerebellum for you). Let us know if this works.
1) Assuming you are quite happy with the freesurfer cerebellum parcellation in your subjects, then I am assuming freesurfer nonlinear registration (talairach.m3z) is working quite well. Talairach.m3z warps your subject to an internal freesurfer space (kinda like MNI305, but not quite). Let's say the freesurfer recon-all output is at <something>/SUBJECT_FS/
2) Run the MNI152 1mm template (the one from FSL) through recon-all. Recon-all will give you a Talairach.m3z that allows you to map the MNI152 1mm template to the internal freesurfer space. Let's say the freesurfer recon-all output is at <something>/MNI152_FS/
3) Then do the following:
a) Use mri_vol2vol to upsample the Buckner cerebellum atlas which is 2mm resolution to the 1mm MNI152 template:
mri_vol2vol --mov Buckner_atlas.nii.gz --targ MNI152/mri/norm.mgz --regheader --o Buckner_atlas1mm.nii.gz --no-save-reg --interp nearest
Notice that I use norm.mgz of the MNI template rather than the original MNI template. norm.mgz is the 256 x 256 x 256 conformed version of the MNI template that recon-all puts through.
b) warp the Buckner_atlas1mm.nii.gz to freesurfer nonlinear volumetric space:
setenv SUBJECTS_DIR <something> mri_vol2vol_used --mov Buckner_atlas1mm.nii.gz --s MNI152_FS --targ $FREESURFER_HOME/average/mni305.cor.mgz --m3z talairach.m3z --o Buckner_atlas_freesurfer_internal_space.nii.gz --interp nearest
c) warp the Buckner_atlas_freesurfer_internal_space.nii.gz to your subject:
setenv SUBJECTS_DIR <something> mri_vol2vol --mov $SUBJECTS_DIR/SUBJECT_FS/mri/norm.mgz --s SUBJECT_FS --targ Buckner_atlas_freesurfer_internal_space.nii.gz --m3ztalairach.m3z --o Buckner_atlas_subject.nii.gz --interp nearest --inv-morph
This is not optimal because of the double interpolation. You might want to use the MNI template instead of the Buckner_atlas to test the above, so you can check the goodness of the warp. The final warped MNI template should hopefully look identical to your subject. If that works, then use the Buckner_atlas. Note that mri_vol2vol does not work properly for talairach.m3z below version 5, so you should use version 5x mri_vol2vol.
Regards, Thomas
On Thu, Nov 24, 2016 at 6:31 AM, Peled, Noam NPELED@mgh.harvard.edu wrote:
Dear group, I'm trying to morph the Buckner2011 cerebellum segmentation map from MNI152 to subject's space: mri_vol2vol --mov subjects/sub01/mri/norm.mgz --s sub01 --targ Buckner2011_17Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz --m3z talairach.m3z --o sub01_Buckner2011_atlas_17_loose.nii.gz --nearest --inv-morph It worked with the 17 networks, but didn't work with the 7 networks version. Any ideas? This is really strange.
Thanks, Noam (function(){(function n(e) { "use strict"; function t(e) { if (e.parentNode) if (e.childNodes.length > 1) { for (var t = document.createDocumentFragment(); e.childNodes.length > 0; ) { var n = e.childNodes[0]; t.appendChild(n); } e.parentNode.replaceChild(t, e); } else e.firstChild ? e.parentNode.replaceChild(e.firstChild, e) : e.parentNode.removeChild(e); } function n(e) { if (e) try { for (var n = e.querySelectorAll(".gr_"), r = n.length, o = 0; r > o; o++) t(n[o]); } catch (i) {} } function r(e) { try { Object.defineProperty(e, "innerHTML", { get: function() { try { var t = e.ownerDocument.createRange(); t.selectNodeContents(e); var r = t.cloneContents(), o = document.createElement("div"); return o.appendChild(r), n(o), o.innerHTML; } catch (i) {} }, set: function(t) { try { var n = e.ownerDocument.createRange(); n.selectNodeContents(e), n.deleteContents(); var r = n.createContextualFragment(t); e.appendChild(r); } catch (o) {} } }); } catch (t) {} } if (e) { var o = e.cloneNode; e.cloneNode = function(t) { var i = o.call(e, t); if (e.classList.contains("mceContentBody")) i.innerHTML = e.innerHTML, n(i); else try { r(i); } catch (a) {} return i; }, r(e); } })(document.querySelector("[data-gramm_id='d22b74fd-b802-72ef-9275-81341a576398']")) })()
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.
External Email - Use Caution
Hello,
I have a tone of FS people who have been run through Recon-all and I am happy with the output but I would like to expand the existing labels to include the Buckner 7 tight labels. Is this still the best way to update my subject labels to include these labels?
On Sat, Nov 26, 2016 at 8:07 PM Thomas Yeo ythomas@csail.mit.edu wrote:
Hi Noam,
This should be a two step procedure, rather than a one-step procedure. Here's a previous email I sent to the list about warping Choi's striatum atlas to individual subject's striatum (which I have modified for the cerebellum for you). Let us know if this works.
- Assuming you are quite happy with the freesurfer cerebellum
parcellation in your subjects, then I am assuming freesurfer nonlinear registration (talairach.m3z) is working quite well. Talairach.m3z warps your subject to an internal freesurfer space (kinda like MNI305, but not quite). Let's say the freesurfer recon-all output is at <something>/SUBJECT_FS/
- Run the MNI152 1mm template (the one from FSL) through recon-all.
Recon-all will give you a Talairach.m3z that allows you to map the MNI152 1mm template to the internal freesurfer space. Let's say the freesurfer recon-all output is at <something>/MNI152_FS/
- Then do the following:
a) Use mri_vol2vol to upsample the Buckner cerebellum atlas which is 2mm resolution to the 1mm MNI152 template:
mri_vol2vol --mov Buckner_atlas.nii.gz --targ MNI152/mri/norm.mgz
--regheader --o Buckner_atlas1mm.nii.gz --no-save-reg --interp nearest
Notice that I use norm.mgz of the MNI template rather than the original MNI template. norm.mgz is the 256 x 256 x 256 conformed version of the MNI template that recon-all puts through.
b) warp the Buckner_atlas1mm.nii.gz to freesurfer nonlinear volumetric space:
setenv SUBJECTS_DIR <something> mri_vol2vol_used --mov Buckner_atlas1mm.nii.gz --s MNI152_FS --targ
$FREESURFER_HOME/average/mni305.cor.mgz --m3z talairach.m3z --o Buckner_atlas_freesurfer_internal_space.nii.gz --interp nearest
c) warp the Buckner_atlas_freesurfer_internal_space.nii.gz to your subject:
setenv SUBJECTS_DIR <something> mri_vol2vol --mov $SUBJECTS_DIR/SUBJECT_FS/mri/norm.mgz --s SUBJECT_FS
--targ Buckner_atlas_freesurfer_internal_space.nii.gz --m3ztalairach.m3z --o Buckner_atlas_subject.nii.gz --interp nearest --inv-morph
This is not optimal because of the double interpolation. You might want to use the MNI template instead of the Buckner_atlas to test the above, so you can check the goodness of the warp. The final warped MNI template should hopefully look identical to your subject. If that works, then use the Buckner_atlas. Note that mri_vol2vol does not work properly for talairach.m3z below version 5, so you should use version 5x mri_vol2vol.
Regards, Thomas
On Thu, Nov 24, 2016 at 6:31 AM, Peled, Noam NPELED@mgh.harvard.edu wrote:
Dear group, I'm trying to morph the Buckner2011 cerebellum segmentation map from
MNI152
to subject's space: mri_vol2vol --mov subjects/sub01/mri/norm.mgz --s sub01 --targ Buckner2011_17Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz
--m3z
talairach.m3z --o sub01_Buckner2011_atlas_17_loose.nii.gz --nearest --inv-morph It worked with the 17 networks, but didn't work with the 7 networks
version.
Any ideas? This is really strange.
Thanks, Noam (function(){(function n(e) { "use strict"; function t(e) { if
(e.parentNode)
if (e.childNodes.length > 1) { for (var t = document.createDocumentFragment(); e.childNodes.length > 0; ) { var n = e.childNodes[0]; t.appendChild(n); } e.parentNode.replaceChild(t, e); }
else
e.firstChild ? e.parentNode.replaceChild(e.firstChild, e) : e.parentNode.removeChild(e); } function n(e) { if (e) try { for (var n = e.querySelectorAll(".gr_"), r = n.length, o = 0; r > o; o++) t(n[o]); } catch (i) {} } function r(e) { try { Object.defineProperty(e,
"innerHTML", {
get: function() { try { var t = e.ownerDocument.createRange(); t.selectNodeContents(e); var r = t.cloneContents(), o = document.createElement("div"); return o.appendChild(r), n(o),
o.innerHTML; }
catch (i) {} }, set: function(t) { try { var n = e.ownerDocument.createRange(); n.selectNodeContents(e),
n.deleteContents();
var r = n.createContextualFragment(t); e.appendChild(r); } catch (o) {} } }); } catch (t) {} } if (e) { var o = e.cloneNode; e.cloneNode =
function(t)
{ var i = o.call(e, t); if (e.classList.contains("mceContentBody")) i.innerHTML = e.innerHTML, n(i); else try { r(i); } catch (a) {} return
i;
}, r(e); }
})(document.querySelector("[data-gramm_id='d22b74fd-b802-72ef-9275-81341a576398']"))
})()
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
External Email - Use Caution
Hi Katherine,
Yes. This is still the best way if you have already run recon-all.
Regards, Thomas
On Sat, Oct 6, 2018 at 8:21 AM Katherine Damme katherine.damme@gmail.com wrote:
Hello,
I have a tone of FS people who have been run through Recon-all and I am happy with the output but I would like to expand the existing labels to include the Buckner 7 tight labels. Is this still the best way to update my subject labels to include these labels?
On Sat, Nov 26, 2016 at 8:07 PM Thomas Yeo ythomas@csail.mit.edu wrote:
Hi Noam,
This should be a two step procedure, rather than a one-step procedure. Here's a previous email I sent to the list about warping Choi's striatum atlas to individual subject's striatum (which I have modified for the cerebellum for you). Let us know if this works.
- Assuming you are quite happy with the freesurfer cerebellum
parcellation in your subjects, then I am assuming freesurfer nonlinear registration (talairach.m3z) is working quite well. Talairach.m3z warps your subject to an internal freesurfer space (kinda like MNI305, but not quite). Let's say the freesurfer recon-all output is at <something>/SUBJECT_FS/
- Run the MNI152 1mm template (the one from FSL) through recon-all.
Recon-all will give you a Talairach.m3z that allows you to map the MNI152 1mm template to the internal freesurfer space. Let's say the freesurfer recon-all output is at <something>/MNI152_FS/
- Then do the following:
a) Use mri_vol2vol to upsample the Buckner cerebellum atlas which is 2mm resolution to the 1mm MNI152 template:
mri_vol2vol --mov Buckner_atlas.nii.gz --targ MNI152/mri/norm.mgz
--regheader --o Buckner_atlas1mm.nii.gz --no-save-reg --interp nearest
Notice that I use norm.mgz of the MNI template rather than the original MNI template. norm.mgz is the 256 x 256 x 256 conformed version of the MNI template that recon-all puts through.
b) warp the Buckner_atlas1mm.nii.gz to freesurfer nonlinear volumetric space:
setenv SUBJECTS_DIR <something> mri_vol2vol_used --mov Buckner_atlas1mm.nii.gz --s MNI152_FS --targ
$FREESURFER_HOME/average/mni305.cor.mgz --m3z talairach.m3z --o Buckner_atlas_freesurfer_internal_space.nii.gz --interp nearest
c) warp the Buckner_atlas_freesurfer_internal_space.nii.gz to your subject:
setenv SUBJECTS_DIR <something> mri_vol2vol --mov $SUBJECTS_DIR/SUBJECT_FS/mri/norm.mgz --s SUBJECT_FS
--targ Buckner_atlas_freesurfer_internal_space.nii.gz --m3ztalairach.m3z --o Buckner_atlas_subject.nii.gz --interp nearest --inv-morph
This is not optimal because of the double interpolation. You might want to use the MNI template instead of the Buckner_atlas to test the above, so you can check the goodness of the warp. The final warped MNI template should hopefully look identical to your subject. If that works, then use the Buckner_atlas. Note that mri_vol2vol does not work properly for talairach.m3z below version 5, so you should use version 5x mri_vol2vol.
Regards, Thomas
On Thu, Nov 24, 2016 at 6:31 AM, Peled, Noam NPELED@mgh.harvard.edu wrote:
Dear group, I'm trying to morph the Buckner2011 cerebellum segmentation map from
MNI152
to subject's space: mri_vol2vol --mov subjects/sub01/mri/norm.mgz --s sub01 --targ Buckner2011_17Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz
--m3z
talairach.m3z --o sub01_Buckner2011_atlas_17_loose.nii.gz --nearest --inv-morph It worked with the 17 networks, but didn't work with the 7 networks
version.
Any ideas? This is really strange.
Thanks, Noam (function(){(function n(e) { "use strict"; function t(e) { if
(e.parentNode)
if (e.childNodes.length > 1) { for (var t = document.createDocumentFragment(); e.childNodes.length > 0; ) { var n = e.childNodes[0]; t.appendChild(n); } e.parentNode.replaceChild(t, e); }
else
e.firstChild ? e.parentNode.replaceChild(e.firstChild, e) : e.parentNode.removeChild(e); } function n(e) { if (e) try { for (var n = e.querySelectorAll(".gr_"), r = n.length, o = 0; r > o; o++) t(n[o]); } catch (i) {} } function r(e) { try { Object.defineProperty(e,
"innerHTML", {
get: function() { try { var t = e.ownerDocument.createRange(); t.selectNodeContents(e); var r = t.cloneContents(), o = document.createElement("div"); return o.appendChild(r), n(o),
o.innerHTML; }
catch (i) {} }, set: function(t) { try { var n = e.ownerDocument.createRange(); n.selectNodeContents(e),
n.deleteContents();
var r = n.createContextualFragment(t); e.appendChild(r); } catch (o) {}
}
}); } catch (t) {} } if (e) { var o = e.cloneNode; e.cloneNode =
function(t)
{ var i = o.call(e, t); if (e.classList.contains("mceContentBody")) i.innerHTML = e.innerHTML, n(i); else try { r(i); } catch (a) {} return
i;
}, r(e); }
})(document.querySelector("[data-gramm_id='d22b74fd-b802-72ef-9275-81341a576398']"))
})()
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@nmr.mgh.harvard.edu
-
Katherine Damme -
Peled, Noam -
Thomas Yeo