Hi experts, I have two (unrelated) issues. I am seeking a command-line method to remove non-cortex vertices and triangles from a surface. I have seen the manual method with tksurfer, but perhaps this is not suitable for larger datasets?
I have tried to use surf2surf for downsampling of the meshes NOT generated by Freesurfer into icosahedron, to no avail, maybe because this command seeks to map the .sulc data which is absent in the alien mesh. Please let me have any advice for this goal if basically possible with available freesurfer tools.
Thanks, Sourena Soheili
Hi Sourena
You can try mris_map_cuts, which I wrote a while ago, but haven't used very much (hopefully it still works!). For the downsampling, I think Rudolph had something. If not, we can modify surf2surf to avoid using the sulc if some flag is specified. Rudolph?
cheers Bruce
On Fri, 13 Jul 2012, Sourena Soheilinezhad wrote:
Hi experts, I have two (unrelated) issues. I am seeking a command-line method to remove non-cortex vertices and triangles from a surface. I have seen the manual method with tksurfer, but perhaps this is not suitable for larger datasets?
I have tried to use surf2surf for downsampling of the meshes NOT generated by Freesurfer into icosahedron, to no avail, maybe because this command seeks to map the .sulc data which is absent in the alien mesh. Please let me have any advice for this goal if basically possible with available freesurfer tools.
Thanks, Sourena Soheili _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Bruce,
Thanks. But when I use mris_map_cuts on the original white surface, the output is: "MRISreadPatch: bad vertex # (1701060705) found in patch file" I guess that some preliminary job should be done before feeding to the command? As an alternative, is it wise to extract all .aparc labels and then merge them with mri_mergelabels to have a single full cortex label file?
(For downsampling, the goal is to bring FSL FIRST subcortical T1 segmentation down to DTI resolution.)
Cheers, Sourena
On 7/14/12, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Sourena
You can try mris_map_cuts, which I wrote a while ago, but haven't used very
much (hopefully it still works!). For the downsampling, I think Rudolph had
something. If not, we can modify surf2surf to avoid using the sulc if some flag is specified. Rudolph?
cheers Bruce
On Fri, 13 Jul 2012, Sourena Soheilinezhad wrote:
Hi experts, I have two (unrelated) issues. I am seeking a command-line method to remove non-cortex vertices and triangles from a surface. I have seen the manual method with tksurfer, but perhaps this is not suitable for larger datasets?
I have tried to use surf2surf for downsampling of the meshes NOT generated by Freesurfer into icosahedron, to no avail, maybe because this command seeks to map the .sulc data which is absent in the alien mesh. Please let me have any advice for this goal if basically possible with available freesurfer tools.
Thanks, Sourena Soheili _______________________________________________ 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.
Hi Sourena
I'll try to take a look this week. As I said it's really an alpha version (if that). If you are downsampling a voxel segmentation why not just use vol2vol?
cheers Bruce
On Sun, 15 Jul 2012, Sourena Soheilinezhad wrote:
Hi Bruce,
Thanks. But when I use mris_map_cuts on the original white surface, the output is: "MRISreadPatch: bad vertex # (1701060705) found in patch file" I guess that some preliminary job should be done before feeding to the command? As an alternative, is it wise to extract all .aparc labels and then merge them with mri_mergelabels to have a single full cortex label file?
(For downsampling, the goal is to bring FSL FIRST subcortical T1 segmentation down to DTI resolution.)
Cheers, Sourena
On 7/14/12, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Sourena
You can try mris_map_cuts, which I wrote a while ago, but haven't used very
much (hopefully it still works!). For the downsampling, I think Rudolph had
something. If not, we can modify surf2surf to avoid using the sulc if some flag is specified. Rudolph?
cheers Bruce
On Fri, 13 Jul 2012, Sourena Soheilinezhad wrote:
Hi experts, I have two (unrelated) issues. I am seeking a command-line method to remove non-cortex vertices and triangles from a surface. I have seen the manual method with tksurfer, but perhaps this is not suitable for larger datasets?
I have tried to use surf2surf for downsampling of the meshes NOT generated by Freesurfer into icosahedron, to no avail, maybe because this command seeks to map the .sulc data which is absent in the alien mesh. Please let me have any advice for this goal if basically possible with available freesurfer tools.
Thanks, Sourena Soheili _______________________________________________ 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.
p.s. I just tried it and it worked for me. Can you send me your command line? Don't give it the white surface as input - it must be a patch. So you have to make the cuts for one subject then map those to others (and run mris_flatten on each one)
cheers Bruce
On Sun, 15 Jul 2012, Bruce Fischl wrote:
Hi Sourena
I'll try to take a look this week. As I said it's really an alpha version (if that). If you are downsampling a voxel segmentation why not just use vol2vol?
cheers Bruce
On Sun, 15 Jul 2012, Sourena Soheilinezhad wrote:
Hi Bruce,
Thanks. But when I use mris_map_cuts on the original white surface, the output is: "MRISreadPatch: bad vertex # (1701060705) found in patch file" I guess that some preliminary job should be done before feeding to the command? As an alternative, is it wise to extract all .aparc labels and then merge them with mri_mergelabels to have a single full cortex label file?
(For downsampling, the goal is to bring FSL FIRST subcortical T1 segmentation down to DTI resolution.)
Cheers, Sourena
On 7/14/12, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Sourena
You can try mris_map_cuts, which I wrote a while ago, but haven't used very
much (hopefully it still works!). For the downsampling, I think Rudolph had
something. If not, we can modify surf2surf to avoid using the sulc if some flag is specified. Rudolph?
cheers Bruce
On Fri, 13 Jul 2012, Sourena Soheilinezhad wrote:
Hi experts, I have two (unrelated) issues. I am seeking a command-line method to remove non-cortex vertices and triangles from a surface. I have seen the manual method with tksurfer, but perhaps this is not suitable for larger datasets?
I have tried to use surf2surf for downsampling of the meshes NOT generated by Freesurfer into icosahedron, to no avail, maybe because this command seeks to map the .sulc data which is absent in the alien mesh. Please let me have any advice for this goal if basically possible with available freesurfer tools.
Thanks, Sourena Soheili _______________________________________________ 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
Hi Bruce, Seems that I have used the command very naively! So as I understand, I have to make the midline cuts manually in tksurfer and remove the non-cortex vertices for one subject. But then how should I pass this reference cortex patch and another subject's surface to the mris_map_cuts? The patch has to be in subject XYZ space for feeding into tractography, (so why mris_flatten?)
About downsampling, it is possible to use vol2vol and stay in the voxel domain, but since most of the subcortical structures (esp. striatum which has high cortical connectivity) encompass low diffusion anisotropy, I guess it should be more efficient to encode the connectivity matrix based on "surface collision" and omit the "inside". (But not sure if DTI resolution renders this efficiency gain significant.)
Cheers, Sourena
On 7/15/12, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
p.s. I just tried it and it worked for me. Can you send me your command line? Don't give it the white surface as input - it must be a patch. So you
have to make the cuts for one subject then map those to others (and run mris_flatten on each one)
cheers Bruce
On Sun, 15 Jul 2012, Bruce Fischl wrote:
Hi Sourena
I'll try to take a look this week. As I said it's really an alpha version (if that). If you are downsampling a voxel segmentation why not just use vol2vol?
cheers Bruce
On Sun, 15 Jul 2012, Sourena Soheilinezhad wrote:
Hi Bruce,
Thanks. But when I use mris_map_cuts on the original white surface, the output is: "MRISreadPatch: bad vertex # (1701060705) found in patch file" I guess that some preliminary job should be done before feeding to the command? As an alternative, is it wise to extract all .aparc labels and then merge them with mri_mergelabels to have a single full cortex label file?
(For downsampling, the goal is to bring FSL FIRST subcortical T1 segmentation down to DTI resolution.)
Cheers, Sourena
On 7/14/12, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Sourena
You can try mris_map_cuts, which I wrote a while ago, but haven't used very
much (hopefully it still works!). For the downsampling, I think Rudolph had
something. If not, we can modify surf2surf to avoid using the sulc if some flag is specified. Rudolph?
cheers Bruce
On Fri, 13 Jul 2012, Sourena Soheilinezhad wrote:
Hi experts, I have two (unrelated) issues. I am seeking a command-line method to remove non-cortex vertices and triangles from a surface. I have seen the manual method with tksurfer, but perhaps this is not suitable for larger datasets?
I have tried to use surf2surf for downsampling of the meshes NOT generated by Freesurfer into icosahedron, to no avail, maybe because this command seeks to map the .sulc data which is absent in the alien mesh. Please let me have any advice for this goal if basically possible with available freesurfer tools.
Thanks, Sourena Soheili _______________________________________________ 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
Hi Sourena
you run it like this:
mris_map_cuts \ $SUBJECTS_DIR/$subject1/surf/lh.patch \ $SUBJECTS_DIR/$subject2/surf/lh.patch
the xyz coords don't really matter as it can't map those. It will map the pattern of cuts to the new subject, which you will then have to flatten.
cheers Bruce
On Sun, 15 Jul 2012, Sourena Soheilinezhad wrote:
Hi Bruce, Seems that I have used the command very naively! So as I understand, I have to make the midline cuts manually in tksurfer and remove the non-cortex vertices for one subject. But then how should I pass this reference cortex patch and another subject's surface to the mris_map_cuts? The patch has to be in subject XYZ space for feeding into tractography, (so why mris_flatten?)
About downsampling, it is possible to use vol2vol and stay in the voxel domain, but since most of the subcortical structures (esp. striatum which has high cortical connectivity) encompass low diffusion anisotropy, I guess it should be more efficient to encode the connectivity matrix based on "surface collision" and omit the "inside". (But not sure if DTI resolution renders this efficiency gain significant.)
Cheers, Sourena
On 7/15/12, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
p.s. I just tried it and it worked for me. Can you send me your command line? Don't give it the white surface as input - it must be a patch. So you
have to make the cuts for one subject then map those to others (and run mris_flatten on each one)
cheers Bruce
On Sun, 15 Jul 2012, Bruce Fischl wrote:
Hi Sourena
I'll try to take a look this week. As I said it's really an alpha version (if that). If you are downsampling a voxel segmentation why not just use vol2vol?
cheers Bruce
On Sun, 15 Jul 2012, Sourena Soheilinezhad wrote:
Hi Bruce,
Thanks. But when I use mris_map_cuts on the original white surface, the output is: "MRISreadPatch: bad vertex # (1701060705) found in patch file" I guess that some preliminary job should be done before feeding to the command? As an alternative, is it wise to extract all .aparc labels and then merge them with mri_mergelabels to have a single full cortex label file?
(For downsampling, the goal is to bring FSL FIRST subcortical T1 segmentation down to DTI resolution.)
Cheers, Sourena
On 7/14/12, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Sourena
You can try mris_map_cuts, which I wrote a while ago, but haven't used very
much (hopefully it still works!). For the downsampling, I think Rudolph had
something. If not, we can modify surf2surf to avoid using the sulc if some flag is specified. Rudolph?
cheers Bruce
On Fri, 13 Jul 2012, Sourena Soheilinezhad wrote:
Hi experts, I have two (unrelated) issues. I am seeking a command-line method to remove non-cortex vertices and triangles from a surface. I have seen the manual method with tksurfer, but perhaps this is not suitable for larger datasets?
I have tried to use surf2surf for downsampling of the meshes NOT generated by Freesurfer into icosahedron, to no avail, maybe because this command seeks to map the .sulc data which is absent in the alien mesh. Please let me have any advice for this goal if basically possible with available freesurfer tools.
Thanks, Sourena Soheili _______________________________________________ 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
p.s. Subcortical FIRST T1 segmentation works on the voxels, but it outputs mesh objects with the vertex numbers in anatomical correspondence across subjects.
On 7/15/12, Sourena Soheilinezhad sourena.soheili@gmail.com wrote:
Hi Bruce, Seems that I have used the command very naively! So as I understand, I have to make the midline cuts manually in tksurfer and remove the non-cortex vertices for one subject. But then how should I pass this reference cortex patch and another subject's surface to the mris_map_cuts? The patch has to be in subject XYZ space for feeding into tractography, (so why mris_flatten?)
About downsampling, it is possible to use vol2vol and stay in the voxel domain, but since most of the subcortical structures (esp. striatum which has high cortical connectivity) encompass low diffusion anisotropy, I guess it should be more efficient to encode the connectivity matrix based on "surface collision" and omit the "inside". (But not sure if DTI resolution renders this efficiency gain significant.)
Cheers, Sourena
On 7/15/12, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
p.s. I just tried it and it worked for me. Can you send me your command line? Don't give it the white surface as input - it must be a patch. So you
have to make the cuts for one subject then map those to others (and run mris_flatten on each one)
cheers Bruce
On Sun, 15 Jul 2012, Bruce Fischl wrote:
Hi Sourena
I'll try to take a look this week. As I said it's really an alpha version (if that). If you are downsampling a voxel segmentation why not just use vol2vol?
cheers Bruce
On Sun, 15 Jul 2012, Sourena Soheilinezhad wrote:
Hi Bruce,
Thanks. But when I use mris_map_cuts on the original white surface, the output is: "MRISreadPatch: bad vertex # (1701060705) found in patch file" I guess that some preliminary job should be done before feeding to the command? As an alternative, is it wise to extract all .aparc labels and then merge them with mri_mergelabels to have a single full cortex label file?
(For downsampling, the goal is to bring FSL FIRST subcortical T1 segmentation down to DTI resolution.)
Cheers, Sourena
On 7/14/12, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Sourena
You can try mris_map_cuts, which I wrote a while ago, but haven't used very
much (hopefully it still works!). For the downsampling, I think Rudolph had
something. If not, we can modify surf2surf to avoid using the sulc if some flag is specified. Rudolph?
cheers Bruce
On Fri, 13 Jul 2012, Sourena Soheilinezhad wrote:
Hi experts, I have two (unrelated) issues. I am seeking a command-line method to remove non-cortex vertices and triangles from a surface. I have seen the manual method with tksurfer, but perhaps this is not suitable for larger datasets?
I have tried to use surf2surf for downsampling of the meshes NOT generated by Freesurfer into icosahedron, to no avail, maybe because this command seeks to map the .sulc data which is absent in the alien mesh. Please let me have any advice for this goal if basically possible with available freesurfer tools.
Thanks, Sourena Soheili _______________________________________________ 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
Seems that I am missing a key concept. A patch is a portion of a surface, and mris_flatten moves the patch vertices (XYZ of every vertex) to make the whole patch planar, right? I would rather need a surface which still lies in gray/white interface. (I have these impressions after reading http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferOccipitalFlattenedPatch)
On 7/15/12, Sourena Soheilinezhad sourena.soheili@gmail.com wrote:
p.s. Subcortical FIRST T1 segmentation works on the voxels, but it outputs mesh objects with the vertex numbers in anatomical correspondence across subjects.
On 7/15/12, Sourena Soheilinezhad sourena.soheili@gmail.com wrote:
Hi Bruce, Seems that I have used the command very naively! So as I understand, I have to make the midline cuts manually in tksurfer and remove the non-cortex vertices for one subject. But then how should I pass this reference cortex patch and another subject's surface to the mris_map_cuts? The patch has to be in subject XYZ space for feeding into tractography, (so why mris_flatten?)
About downsampling, it is possible to use vol2vol and stay in the voxel domain, but since most of the subcortical structures (esp. striatum which has high cortical connectivity) encompass low diffusion anisotropy, I guess it should be more efficient to encode the connectivity matrix based on "surface collision" and omit the "inside". (But not sure if DTI resolution renders this efficiency gain significant.)
Cheers, Sourena
On 7/15/12, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
p.s. I just tried it and it worked for me. Can you send me your command line? Don't give it the white surface as input - it must be a patch. So you
have to make the cuts for one subject then map those to others (and run mris_flatten on each one)
cheers Bruce
On Sun, 15 Jul 2012, Bruce Fischl wrote:
Hi Sourena
I'll try to take a look this week. As I said it's really an alpha version (if that). If you are downsampling a voxel segmentation why not just use vol2vol?
cheers Bruce
On Sun, 15 Jul 2012, Sourena Soheilinezhad wrote:
Hi Bruce,
Thanks. But when I use mris_map_cuts on the original white surface, the output is: "MRISreadPatch: bad vertex # (1701060705) found in patch file" I guess that some preliminary job should be done before feeding to the command? As an alternative, is it wise to extract all .aparc labels and then merge them with mri_mergelabels to have a single full cortex label file?
(For downsampling, the goal is to bring FSL FIRST subcortical T1 segmentation down to DTI resolution.)
Cheers, Sourena
On 7/14/12, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Sourena
You can try mris_map_cuts, which I wrote a while ago, but haven't used very
much (hopefully it still works!). For the downsampling, I think Rudolph had
something. If not, we can modify surf2surf to avoid using the sulc if some flag is specified. Rudolph?
cheers Bruce
On Fri, 13 Jul 2012, Sourena Soheilinezhad wrote:
> Hi experts, > I have two (unrelated) issues. > I am seeking a command-line method to remove non-cortex vertices and > triangles from a surface. I have seen the manual method with > tksurfer, > but perhaps this is not suitable for larger datasets? > > I have tried to use surf2surf for downsampling of the meshes NOT > generated by Freesurfer into icosahedron, to no avail, maybe because > this command seeks to map the .sulc data which is absent in the > alien > mesh. Please let me have any advice for this goal if basically > possible with available freesurfer tools. > > Thanks, > Sourena Soheili > _______________________________________________ > 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
Hi Sourena
the flattening is for visualization, and if you don't care about that you can skip it. The patch format is simply a portion of a surface, it doesn't have to be in 2D, so you could cut out the cortex, or even use label2patch with our cortex label to automatically create a cortex patch for each subject. I'm still not entirely sure what you are trying to do, but that might be easier.
cheers Bruce
On Sun, 15 Jul 2012, Sourena Soheilinezhad wrote:
Seems that I am missing a key concept. A patch is a portion of a surface, and mris_flatten moves the patch vertices (XYZ of every vertex) to make the whole patch planar, right? I would rather need a surface which still lies in gray/white interface. (I have these impressions after reading http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferOccipitalFlattenedPatch)
On 7/15/12, Sourena Soheilinezhad sourena.soheili@gmail.com wrote:
p.s. Subcortical FIRST T1 segmentation works on the voxels, but it outputs mesh objects with the vertex numbers in anatomical correspondence across subjects.
On 7/15/12, Sourena Soheilinezhad sourena.soheili@gmail.com wrote:
Hi Bruce, Seems that I have used the command very naively! So as I understand, I have to make the midline cuts manually in tksurfer and remove the non-cortex vertices for one subject. But then how should I pass this reference cortex patch and another subject's surface to the mris_map_cuts? The patch has to be in subject XYZ space for feeding into tractography, (so why mris_flatten?)
About downsampling, it is possible to use vol2vol and stay in the voxel domain, but since most of the subcortical structures (esp. striatum which has high cortical connectivity) encompass low diffusion anisotropy, I guess it should be more efficient to encode the connectivity matrix based on "surface collision" and omit the "inside". (But not sure if DTI resolution renders this efficiency gain significant.)
Cheers, Sourena
On 7/15/12, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
p.s. I just tried it and it worked for me. Can you send me your command line? Don't give it the white surface as input - it must be a patch. So you
have to make the cuts for one subject then map those to others (and run mris_flatten on each one)
cheers Bruce
On Sun, 15 Jul 2012, Bruce Fischl wrote:
Hi Sourena
I'll try to take a look this week. As I said it's really an alpha version (if that). If you are downsampling a voxel segmentation why not just use vol2vol?
cheers Bruce
On Sun, 15 Jul 2012, Sourena Soheilinezhad wrote:
Hi Bruce,
Thanks. But when I use mris_map_cuts on the original white surface, the output is: "MRISreadPatch: bad vertex # (1701060705) found in patch file" I guess that some preliminary job should be done before feeding to the command? As an alternative, is it wise to extract all .aparc labels and then merge them with mri_mergelabels to have a single full cortex label file?
(For downsampling, the goal is to bring FSL FIRST subcortical T1 segmentation down to DTI resolution.)
Cheers, Sourena
On 7/14/12, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: > Hi Sourena > > You can try mris_map_cuts, which I wrote a while ago, but haven't > used > very > > much (hopefully it still works!). For the downsampling, I think > Rudolph > had > > something. If not, we can modify surf2surf to avoid using the sulc if > some > flag is specified. Rudolph? > > cheers > Bruce > > > > On Fri, 13 Jul 2012, Sourena Soheilinezhad wrote: > >> Hi experts, >> I have two (unrelated) issues. >> I am seeking a command-line method to remove non-cortex vertices and >> triangles from a surface. I have seen the manual method with >> tksurfer, >> but perhaps this is not suitable for larger datasets? >> >> I have tried to use surf2surf for downsampling of the meshes NOT >> generated by Freesurfer into icosahedron, to no avail, maybe because >> this command seeks to map the .sulc data which is absent in the >> alien >> mesh. Please let me have any advice for this goal if basically >> possible with available freesurfer tools. >> >> Thanks, >> Sourena Soheili >> _______________________________________________ >> 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
-
Bruce Fischl -
Sourena Soheilinezhad