Hi All,
I wanted to get peoples advice on the best method of registration/interpolation to use on a manually traced segmentation (and its structural) that is not in the same space and orientation as the structurals I started Freesurfer with (although they both originally came from the same image. I want to maintain the integrity of the manual traced binary mask through this registration and reslice. For a number of reasons, I do not want to take Freesurfers output to the space of the manual segmentation.
What do people think is a good technique? Flirt nearest neighbor interpolation? Something different from Freesurfer? ANTs? - Josh
Can you compute the registration between the manually traced anat space and the FS conformed space? Eg, with BBR. If you can do that, then you can run mri_label2vol to convert the mask into FS conformed space (assuming that that is what you want to do). doug
On 03/22/2013 04:43 PM, Joshua Lee wrote:
Hi All,
I wanted to get peoples advice on the best method of registration/interpolation to use on a manually traced segmentation (and its structural) that is not in the same space and orientation as the structurals I started Freesurfer with (although they both originally came from the same image. I want to maintain the integrity of the manual traced binary mask through this registration and reslice. For a number of reasons, I do not want to take Freesurfers output to the space of the manual segmentation.
What do people think is a good technique? Flirt nearest neighbor interpolation? Something different from Freesurfer? ANTs?
Josh
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug. That was in fact what I decided to do.
Thanks!
Josh - J
On Mon, Mar 25, 2013 at 7:38 AM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
Can you compute the registration between the manually traced anat space and the FS conformed space? Eg, with BBR. If you can do that, then you can run mri_label2vol to convert the mask into FS conformed space (assuming that that is what you want to do). doug
On 03/22/2013 04:43 PM, Joshua Lee wrote:
Hi All,
I wanted to get peoples advice on the best method of registration/interpolation to use on a manually traced segmentation (and its structural) that is not in the same space and orientation as the structurals I started Freesurfer with (although they both originally came from the same image. I want to maintain the integrity of the manual traced binary mask through this registration and reslice. For a number of reasons, I do not want to take Freesurfers output to the space of the manual segmentation.
What do people think is a good technique? Flirt nearest neighbor interpolation? Something different from Freesurfer? ANTs?
Josh
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 greve@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 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.
Hi Doug,
Is a standard 12 affine registration sufficient to get a subjects structural (in a different orientation) into the same space as norm.mgz, or will I need some non-linear registration? Basically, what kind of transforms are applied to go from orig to norm? - Joshua Lee Graduate Student Center for Mind and Brain & Department of Psychology University of California, Davis 530.747.3805
On Mon, Mar 25, 2013 at 10:52 AM, Joshua Lee jkilee@ucdavis.edu wrote:
Hi Doug. That was in fact what I decided to do.
Thanks!
Josh
J
On Mon, Mar 25, 2013 at 7:38 AM, Douglas N Greve < greve@nmr.mgh.harvard.edu> wrote:
Can you compute the registration between the manually traced anat space and the FS conformed space? Eg, with BBR. If you can do that, then you can run mri_label2vol to convert the mask into FS conformed space (assuming that that is what you want to do). doug
On 03/22/2013 04:43 PM, Joshua Lee wrote:
Hi All,
I wanted to get peoples advice on the best method of registration/interpolation to use on a manually traced segmentation (and its structural) that is not in the same space and orientation as the structurals I started Freesurfer with (although they both originally came from the same image. I want to maintain the integrity of the manual traced binary mask through this registration and reslice. For a number of reasons, I do not want to take Freesurfers output to the space of the manual segmentation.
What do people think is a good technique? Flirt nearest neighbor interpolation? Something different from Freesurfer? ANTs?
Josh
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 greve@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 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.
Hi Josh,
there are no spatial transforms to go from orig to norm. They are in the same space.
cheers Bruce
On Mon, 25 Mar 2013, Joshua Lee wrote:
Hi Doug,
Is a standard 12 affine registration sufficient to get a subjects structural (in a different orientation) into the same space as norm.mgz, or will I need some non-linear registration? Basically, what kind of transforms are applied to go from orig to norm?
Joshua Lee Graduate Student Center for Mind and Brain & Department of Psychology University of California, Davis 530.747.3805
On Mon, Mar 25, 2013 at 10:52 AM, Joshua Lee jkilee@ucdavis.edu wrote: Hi Doug. That was in fact what I decided to do.
Thanks! Josh -J
On Mon, Mar 25, 2013 at 7:38 AM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
Can you compute the registration between the manually traced anat space and the FS conformed space? Eg, with BBR. If you can do that, then you can run mri_label2vol to convert the mask into FS conformed space (assuming that that is what you want to do). doug On 03/22/2013 04:43 PM, Joshua Lee wrote: > Hi All, > > I wanted to get peoples advice on the best method of > registration/interpolation to use on a manually traced segmentation > (and its structural) that is not in the same space and orientation as > the structurals I started Freesurfer with (although they both > originally came from the same image. I want to maintain the integrity > of the manual traced binary mask through this registration and > reslice. For a number of reasons, I do not want to take Freesurfers > output to the space of the manual segmentation. > > What do people think is a good technique? Flirt nearest neighbor > interpolation? Something different from Freesurfer? ANTs? > - > Josh > >
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 greve@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 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.
yes, the "norm" means intensity normalized, not spatially normalized:) doug
On 03/25/2013 04:56 PM, Bruce Fischl wrote:
Hi Josh,
there are no spatial transforms to go from orig to norm. They are in the same space.
cheers Bruce
On Mon, 25 Mar 2013, Joshua Lee wrote:
Hi Doug,
Is a standard 12 affine registration sufficient to get a subjects structural (in a different orientation) into the same space as norm.mgz, or will I need some non-linear registration? Basically, what kind of transforms are applied to go from orig to norm?
Joshua Lee Graduate Student Center for Mind and Brain & Department of Psychology University of California, Davis 530.747.3805
On Mon, Mar 25, 2013 at 10:52 AM, Joshua Lee jkilee@ucdavis.edu wrote: Hi Doug. That was in fact what I decided to do.
Thanks! Josh -J
On Mon, Mar 25, 2013 at 7:38 AM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
Can you compute the registration between the manually traced anat space and the FS conformed space? Eg, with BBR. If you can do that, then you can run mri_label2vol to convert the mask into FS conformed space (assuming that that is what you want to do). doug On 03/22/2013 04:43 PM, Joshua Lee wrote: > Hi All, > > I wanted to get peoples advice on the best method of > registration/interpolation to use on a manually traced segmentation > (and its structural) that is not in the same space and orientation as > the structurals I started Freesurfer with (although they both > originally came from the same image. I want to maintain the integrity > of the manual traced binary mask through this registration and > reslice. For a number of reasons, I do not want to take Freesurfers > output to the space of the manual segmentation. > > What do people think is a good technique? Flirt nearest neighbor > interpolation? Something different from Freesurfer? ANTs? > - > Josh > >
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 greve@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 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.
I see. To clarify. orig is the conformed version of the original input file, which means just sampling to 1 mm as needed, and cropping to 256 matrix. norm.mgz has some intensity corrections, but does not include spatial changes.
I had read http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat and I thought that maybe that spatial warping was involved beyond resampling to the original dimensions/resolution to get to "native space". This simplifies things greatly. Thank you both.
On Mon, Mar 25, 2013 at 1:56 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
Hi Josh,
there are no spatial transforms to go from orig to norm. They are in the same space.
cheers Bruce
On Mon, 25 Mar 2013, Joshua Lee wrote:
Hi Doug,
Is a standard 12 affine registration sufficient to get a subjects structural (in a different orientation) into the same space as norm.mgz, or will I need some non-linear registration? Basically, what kind of transforms are applied to go from orig to norm?
Joshua Lee Graduate Student Center for Mind and Brain & Department of Psychology University of California, Davis 530.747.3805
On Mon, Mar 25, 2013 at 10:52 AM, Joshua Lee jkilee@ucdavis.edu wrote: Hi Doug. That was in fact what I decided to do.
Thanks! Josh -J
On Mon, Mar 25, 2013 at 7:38 AM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
Can you compute the registration between the manually traced anat space and the FS conformed space? Eg, with BBR. If you can do that, then you can run mri_label2vol to convert the mask into FS conformed space (assuming that that is what you want to do). doug On 03/22/2013 04:43 PM, Joshua Lee wrote: > Hi All, > > I wanted to get peoples advice on the best method of > registration/interpolation to use on a manually traced segmentation > (and its structural) that is not in the same space and orientation as > the structurals I started Freesurfer with (although they both > originally came from the same image. I want to maintain the integrity > of the manual traced binary mask through this registration and > reslice. For a number of reasons, I do not want to take Freesurfers > output to the space of the manual segmentation. > > What do people think is a good technique? Flirt nearest neighbor > interpolation? Something different from Freesurfer? ANTs? > - > Josh > >______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**greve/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/**freesurferhttps://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/**compliancelinehttp://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.
the orig.mgz is also changed to 1 byte/voxel. The norm.mgz is in the same space, but with the skull removed and the subcortical intensity normalization run on it. All the volumes in fact in the mri dir except rawavg.mgz are in the same coords
cheers Bruce
On Mon, 25 Mar 2013, Joshua Lee wrote:
I see. To clarify. orig is the conformed version of the original input file, which means just sampling to 1 mm as needed, and cropping to 256 matrix. norm.mgz has some intensity corrections, but does not include spatial changes.
I had read http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat and I thought that maybe that spatial warping was involved beyond resampling to the original dimensions/resolution to get to "native space". This simplifies things greatly. Thank you both.
On Mon, Mar 25, 2013 at 1:56 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Josh,
there are no spatial transforms to go from orig to norm. They are in the same space. cheers Bruce On Mon, 25 Mar 2013, Joshua Lee wrote: Hi Doug, Is a standard 12 affine registration sufficient to get a subjects structural (in a different orientation) into the same space as norm.mgz, or will I need some non-linear registration? Basically, what kind of transforms are applied to go from orig to norm? - Joshua Lee Graduate Student Center for Mind and Brain & Department of Psychology University of California, Davis 530.747.3805 On Mon, Mar 25, 2013 at 10:52 AM, Joshua Lee <jkilee@ucdavis.edu> wrote: Hi Doug. That was in fact what I decided to do. Thanks! Josh - J On Mon, Mar 25, 2013 at 7:38 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote: Can you compute the registration between the manually traced anat space and the FS conformed space? Eg, with BBR. If you can do that, then you can run mri_label2vol to convert the mask into FS conformed space (assuming that that is what you want to do). doug On 03/22/2013 04:43 PM, Joshua Lee wrote: > Hi All, > > I wanted to get peoples advice on the best method of > registration/interpolation to use on a manually traced segmentation > (and its structural) that is not in the same space and orientation as > the structurals I started Freesurfer with (although they both > originally came from the same image. I want to maintain the integrity > of the manual traced binary mask through this registration and > reslice. For a number of reasons, I do not want to take Freesurfers > output to the space of the manual segmentation. > > What do people think is a good technique? Flirt nearest neighbor > interpolation? Something different from Freesurfer? ANTs? > - > Josh > > > _______________________________________________ > 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 greve@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 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@nmr.mgh.harvard.edu
-
Bruce Fischl -
Douglas N Greve -
Joshua Lee