Re: [Freesurfer] ribbon volumes
Almost. This will include medial wall voxels that are not GM. It will also not include subcort GM. It is better to use aparc+aseg.mgz and merge the GM ROIs together. On 1/15/17 1:01 AM, Zhivago wrote: Hi, Are the lh.ribbon & rh.ribbon volumes the GM estimate from reconall? Can I used these as GM voxels? Thanks, Zhivago... ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ 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] ribbon volumes
yes, I believe so On Sun, 15 Jan 2017, Zhivago wrote: Hi, Are the lh.ribbon & rh.ribbon volumes the GM estimate from reconall? Can I used these as GM voxels? Thanks, Zhivago... ___ 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] ribbon volumes
Hi, Are the lh.ribbon & rh.ribbon volumes the GM estimate from reconall? Can I used these as GM voxels? Thanks, Zhivago... ___ 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] ribbon label volume mapping
Doug - thanks that sounds well worth trying. the labels we have have arbitrary spatial resolution in the saggital plane, and 1mm gaps between saggital slices. In general in this project we are using an isotropic resolution of 0.25mm. To generate surfaces in freesurfer I have to downsample to 0.35mm (to fit into 256) in applying the procedure you suggest a) is it possible to use a volume with a dimension 256? b) is it possible to use a non-isotropic resolution? playing around with non-isotropic resolutions, projection fractions and vote would yield different results. c) can mri_aparc2aseg output a volume 256? 0.35 isotropic will be ok. we'd prefer 0.25 if we can. best Colin -- Forwarded message -- From: Douglas Greve gr...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Cc: Date: Sun, 23 Jun 2013 20:03:09 -0700 Subject: Re: [Freesurfer] ribbon label volume mapping You could run mri_vol2surf at different projection fractions (and using nearest neighbor interp). This will create a set of files, one for each projection fraction. You can then run mri_concat with the --vote option to get you the most frequently occurring label. You could then use mris_seg2annot to create an annotation. If you want to go the other way, you will need to combine your labels into an annotation (mris_label2annot), then convert that into a volume with mri_aparc2aseg. doug On 6/22/13 10:08 AM, Colin Reveley wrote: If one has a volume of integers, each representing a cortical area, can one map that to the surface as a set of labels, in a smart way that e.g. takes the mode of the voxels that lie on the vector between equivalent white and pial nodes (ie uses curvature and thickness information, tacitly or explicitly)? the labels are not exactly on the ribbon. There are many voxels outside the ribbon that are non zero. Like caudate etc. and some voxels that are within the ribbon but are zero because the label data is was/is non-isotropic originally (which is the problem we want to solve in fact). that would be great. Now let's say you already have labels on a mesh. can you generate a ribbon volume of labels, i.e. the opposite operation to what I enquire about above (opposite but not inverse operation)? This is work in rhesus. So my pipeline is very barebones indeed, really just mri_normalize ... mri_tesselate mri_inflate/smooth/sphere mris_fix_topology -noaseg -noaprc mris_make_surfaces -naseg -noaparc I only have access to what is generated by that sequence or what I can subsequently generate. I can generate a freesurfer like ribbon with mris_fill. My understanding of labels and data mapping in general in freesurfer is very poor. Maybe adapting one of your matlab scripts might be an idea, if there is not another way? many thanks, Colin, Sussex ___ Freesurfer mailing listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ 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] ribbon label volume mapping
On 06/25/2013 12:12 PM, Colin Reveley wrote: Doug - thanks that sounds well worth trying. the labels we have have arbitrary spatial resolution in the saggital plane, and 1mm gaps between saggital slices. In general in this project we are using an isotropic resolution of 0.25mm. To generate surfaces in freesurfer I have to downsample to 0.35mm (to fit into 256) in applying the procedure you suggest a) is it possible to use a volume with a dimension 256? yes, you just have to have an accurate registration b) is it possible to use a non-isotropic resolution? yes playing around with non-isotropic resolutions, projection fractions and vote would yield different results. c) can mri_aparc2aseg output a volume 256? I don't think so. But you can use mri_label2vol to map the 256 to your volume, though you will probably lose some resolution 0.35 isotropic will be ok. we'd prefer 0.25 if we can. best Colin -- Forwarded message -- From: Douglas Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu Cc: Date: Sun, 23 Jun 2013 20:03:09 -0700 Subject: Re: [Freesurfer] ribbon label volume mapping You could run mri_vol2surf at different projection fractions (and using nearest neighbor interp). This will create a set of files, one for each projection fraction. You can then run mri_concat with the --vote option to get you the most frequently occurring label. You could then use mris_seg2annot to create an annotation. If you want to go the other way, you will need to combine your labels into an annotation (mris_label2annot), then convert that into a volume with mri_aparc2aseg. doug On 6/22/13 10:08 AM, Colin Reveley wrote: If one has a volume of integers, each representing a cortical area, can one map that to the surface as a set of labels, in a smart way that e.g. takes the mode of the voxels that lie on the vector between equivalent white and pial nodes (ie uses curvature and thickness information, tacitly or explicitly)? the labels are not exactly on the ribbon. There are many voxels outside the ribbon that are non zero. Like caudate etc. and some voxels that are within the ribbon but are zero because the label data is was/is non-isotropic originally (which is the problem we want to solve in fact). that would be great. Now let's say you already have labels on a mesh. can you generate a ribbon volume of labels, i.e. the opposite operation to what I enquire about above (opposite but not inverse operation)? This is work in rhesus. So my pipeline is very barebones indeed, really just mri_normalize ... mri_tesselate mri_inflate/smooth/sphere mris_fix_topology -noaseg -noaprc mris_make_surfaces -naseg -noaparc I only have access to what is generated by that sequence or what I can subsequently generate. I can generate a freesurfer like ribbon with mris_fill. My understanding of labels and data mapping in general in freesurfer is very poor. Maybe adapting one of your matlab scripts might be an idea, if there is not another way? many thanks, Colin, Sussex ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ 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.
Re: [Freesurfer] ribbon label volume mapping
You could run mri_vol2surf at different projection fractions (and using nearest neighbor interp). This will create a set of files, one for each projection fraction. You can then run mri_concat with the --vote option to get you the most frequently occurring label. You could then use mris_seg2annot to create an annotation. If you want to go the other way, you will need to combine your labels into an annotation (mris_label2annot), then convert that into a volume with mri_aparc2aseg. doug On 6/22/13 10:08 AM, Colin Reveley wrote: If one has a volume of integers, each representing a cortical area, can one map that to the surface as a set of labels, in a smart way that e.g. takes the mode of the voxels that lie on the vector between equivalent white and pial nodes (ie uses curvature and thickness information, tacitly or explicitly)? the labels are not exactly on the ribbon. There are many voxels outside the ribbon that are non zero. Like caudate etc. and some voxels that are within the ribbon but are zero because the label data is was/is non-isotropic originally (which is the problem we want to solve in fact). that would be great. Now let's say you already have labels on a mesh. can you generate a ribbon volume of labels, i.e. the opposite operation to what I enquire about above (opposite but not inverse operation)? This is work in rhesus. So my pipeline is very barebones indeed, really just mri_normalize ... mri_tesselate mri_inflate/smooth/sphere mris_fix_topology -noaseg -noaprc mris_make_surfaces -naseg -noaparc I only have access to what is generated by that sequence or what I can subsequently generate. I can generate a freesurfer like ribbon with mris_fill. My understanding of labels and data mapping in general in freesurfer is very poor. Maybe adapting one of your matlab scripts might be an idea, if there is not another way? many thanks, Colin, Sussex ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ 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] Ribbon
You can try mris_volmask \ --label_left_white 2 --label_left_ribbon 3 \ --label_right_white 41 --label_right_ribbon 42 \ --save_ribbon $subjid doug On 07/08/2012 01:18 PM, Matt Glasser wrote: Hi Bruce, He just needs the grey matter part of a typical ribbon.mgz volume. He lost some of his recon-all folder. Peace, Matt. -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Sunday, July 08, 2012 12:17 PM To: Colin Reveley Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Ribbon Hi Colin what is the representation you want in the end? You can also fill the interior of the surfaces using mris_fill then do some boolean algebra on the results of e.g. the white and pial interiors. cheers Bruce On Sun, 8 Jul 2012, Colin Reveley wrote: Hi - I need to make a ribbon volume. I have all the necessary surfaces, but I'm lacking an aseg.mgz because the data is monkey. I saw one guy on the list had success by just calling his orig.mgz aseg.mgz. I tried that, and it calculated the left right pial and white distances. Men sadly it segfaulted. The program mri_ribbon will give me separate left and white gm ribbons. I combined those, coloured them 3 and 42 and did my level best to fill the wm with the right values, but some bits are wrong. What I'm actually trying to do is use matt glassers myelin mapping in caret. other things could be wrong than my ribbon estimate. If anyone has an idea how to make a good ribbon without aseg I'd appreciate it. Please bear in mind I may be missing much of what one gets when one runs recon-all. I have thickness, curv, surfaces, filled.mgz, pretesselstion wm.mgz not so much else. The filled.mgz doesn't fill all non cortex the way the bert ribbon does, so it's not that useful. Thanks, Colin ___ 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ 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] Ribbon
Hi - I need to make a ribbon volume. I have all the necessary surfaces, but I'm lacking an aseg.mgz because the data is monkey. I saw one guy on the list had success by just calling his orig.mgz aseg.mgz. I tried that, and it calculated the left right pial and white distances. Men sadly it segfaulted. The program mri_ribbon will give me separate left and white gm ribbons. I combined those, coloured them 3 and 42 and did my level best to fill the wm with the right values, but some bits are wrong. What I'm actually trying to do is use matt glassers myelin mapping in caret. other things could be wrong than my ribbon estimate. If anyone has an idea how to make a good ribbon without aseg I'd appreciate it. Please bear in mind I may be missing much of what one gets when one runs recon-all. I have thickness, curv, surfaces, filled.mgz, pretesselstion wm.mgz not so much else. The filled.mgz doesn't fill all non cortex the way the bert ribbon does, so it's not that useful. Thanks, Colin ___ 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] Ribbon
Hi Colin what is the representation you want in the end? You can also fill the interior of the surfaces using mris_fill then do some boolean algebra on the results of e.g. the white and pial interiors. cheers Bruce On Sun, 8 Jul 2012, Colin Reveley wrote: Hi - I need to make a ribbon volume. I have all the necessary surfaces, but I'm lacking an aseg.mgz because the data is monkey. I saw one guy on the list had success by just calling his orig.mgz aseg.mgz. I tried that, and it calculated the left right pial and white distances. Men sadly it segfaulted. The program mri_ribbon will give me separate left and white gm ribbons. I combined those, coloured them 3 and 42 and did my level best to fill the wm with the right values, but some bits are wrong. What I'm actually trying to do is use matt glassers myelin mapping in caret. other things could be wrong than my ribbon estimate. If anyone has an idea how to make a good ribbon without aseg I'd appreciate it. Please bear in mind I may be missing much of what one gets when one runs recon-all. I have thickness, curv, surfaces, filled.mgz, pretesselstion wm.mgz not so much else. The filled.mgz doesn't fill all non cortex the way the bert ribbon does, so it's not that useful. Thanks, Colin ___ 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] Ribbon
Hi Bruce, He just needs the grey matter part of a typical ribbon.mgz volume. He lost some of his recon-all folder. Peace, Matt. -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Sunday, July 08, 2012 12:17 PM To: Colin Reveley Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Ribbon Hi Colin what is the representation you want in the end? You can also fill the interior of the surfaces using mris_fill then do some boolean algebra on the results of e.g. the white and pial interiors. cheers Bruce On Sun, 8 Jul 2012, Colin Reveley wrote: Hi - I need to make a ribbon volume. I have all the necessary surfaces, but I'm lacking an aseg.mgz because the data is monkey. I saw one guy on the list had success by just calling his orig.mgz aseg.mgz. I tried that, and it calculated the left right pial and white distances. Men sadly it segfaulted. The program mri_ribbon will give me separate left and white gm ribbons. I combined those, coloured them 3 and 42 and did my level best to fill the wm with the right values, but some bits are wrong. What I'm actually trying to do is use matt glassers myelin mapping in caret. other things could be wrong than my ribbon estimate. If anyone has an idea how to make a good ribbon without aseg I'd appreciate it. Please bear in mind I may be missing much of what one gets when one runs recon-all. I have thickness, curv, surfaces, filled.mgz, pretesselstion wm.mgz not so much else. The filled.mgz doesn't fill all non cortex the way the bert ribbon does, so it's not that useful. Thanks, Colin ___ 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.
