Hi, FreeSurfer experts
I have a question regarding coregistering white and pial surfaces with the brain.mgz and would appreciate your help on this. I am working on non-human primates and noticed that my white and pial surfaces do not have identical positions as brain.mgz. For example, when I used "mris_fill" to write white and pial surfaces into volume files, they do not have same sto_xyz and qto_xyz values as these in the brain.mgz. This is not the case for human data. So my questions are:
(1) how could I find a transformation matrix between the two, so that when I am using surface-based tractography in the future, the program can find the correspondence between the points on the surfaces and those in the volumetric diffusion MRI data?
(2) How in the future, can I avoid such misregistrations in generating non-human primate surface files in FreeSurfer?
Thank you very much in advance!
Longchuan
Hi Longchuan
have you tried the -cm (conform to min) option in recon-all?
cheers Bruce
On Sun, 18 Nov 2012, Longchuan Li wrote:
Hi, FreeSurfer experts
I have a question regarding coregistering white and pial surfaces with the brain.mgz and would appreciate your help on this. I am working on non-human primates and noticed that my white and pial surfaces do not have identical positions as brain.mgz. For example, when I used "mris_fill" to write white and pial surfaces into volume files, they do not have same sto_xyz and qto_xyz values as these in the brain.mgz. This is not the case for human data. So my questions are:
(1) how could I find a transformation matrix between the two, so that when I am using surface-based tractography in the future, the program can find the correspondence between the points on the surfaces and those in the volumetric diffusion MRI data?
(2) How in the future, can I avoid such misregistrations in generating non-human primate surface files in FreeSurfer?
Thank you very much in advance!
Longchuan
Hi, Bruce
Thank you for the information. I will re-run recon-all using "-cm" option to see if the problem will be solved. In the mean time, do you have any suggestions regarding finding a transformation between the mismatched surfaces and the volume?
Thanks again.
Longchuan
________________________________ From: Bruce Fischl fischl@nmr.mgh.harvard.edu To: Longchuan Li leonado78@yahoo.com Cc: FreeSurfer freesurfer@nmr.mgh.harvard.edu Sent: Monday, November 19, 2012 8:57 AM Subject: Re: [Freesurfer] the positions of white/pial surfaces and the brain.mgz
Hi Longchuan
have you tried the -cm (conform to min) option in recon-all?
cheers Bruce
On Sun, 18 Nov 2012, Longchuan Li wrote:
Hi, FreeSurfer experts
I have a question regarding coregistering white and pial surfaces with the brain.mgz and would appreciate your help on this. I am working on non-human primates and noticed that my white and pial surfaces do not have identical positions as brain.mgz. For example, when I used "mris_fill" to write white and pial surfaces into volume files, they do not have same sto_xyz and qto_xyz values as these in the brain.mgz. This is not the case for human data. So my questions are:
(1) how could I find a transformation matrix between the two, so that when I am using surface-based tractography in the future, the program can find the correspondence between the points on the surfaces and those in the volumetric diffusion MRI data?
(2) How in the future, can I avoid such misregistrations in generating non-human primate surface files in FreeSurfer?
Thank you very much in advance!
Longchuan
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 Longchuan
yes, I think you can do this with tkregister2. Doug can give you the details Bruce On Mon, 19 Nov 2012, Longchuan Li wrote:
Hi, Bruce
Thank you for the information. I will re-run recon-all using "-cm" option to see if the problem will be solved. In the mean time, do you have any suggestions regarding finding a transformation between the mismatched surfaces and the volume?
Thanks again.
Longchuan
From: Bruce Fischl fischl@nmr.mgh.harvard.edu To: Longchuan Li leonado78@yahoo.com Cc: FreeSurfer freesurfer@nmr.mgh.harvard.edu Sent: Monday, November 19, 2012 8:57 AM Subject: Re: [Freesurfer] the positions of white/pial surfaces and the brain.mgz
Hi Longchuan
have you tried the -cm (conform to min) option in recon-all?
cheers Bruce
On Sun, 18 Nov 2012, Longchuan Li wrote:
Hi, FreeSurfer experts
I have a question regarding coregistering white and pial surfaces with the
brain.mgz and would appreciate your help on this. I
am working on non-human primates and noticed that my white and pial
surfaces do not have identical positions as brain.mgz. For
example, when I used "mris_fill" to write white and pial surfaces into
volume files, they do not have same sto_xyz and qto_xyz
values as these in the brain.mgz. This is not the case for human data. So
my questions are:
(1) how could I find a transformation matrix between the two, so that when
I am using surface-based tractography in the future,
the program can find the correspondence between the points on the surfaces
and those in the volumetric diffusion MRI data?
(2) How in the future, can I avoid such misregistrations in generating
non-human primate surface files in FreeSurfer?
Thank you very much in advance!
Longchuan
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.
use bbregister, something like bbregister --s subjectname --init-fsl --t2 --mov lowb.nii --reg register.dat where lowb is the low b (usually b=0) volume from your DTI, the one that you used as the template for motion correction. doug
On 11/19/2012 10:30 AM, Bruce Fischl wrote:
Hi Longchuan
yes, I think you can do this with tkregister2. Doug can give you the details Bruce On Mon, 19 Nov 2012, Longchuan Li wrote:
Hi, Bruce
Thank you for the information. I will re-run recon-all using "-cm" option to see if the problem will be solved. In the mean time, do you have any suggestions regarding finding a transformation between the mismatched surfaces and the volume?
Thanks again.
Longchuan
From: Bruce Fischl fischl@nmr.mgh.harvard.edu To: Longchuan Li leonado78@yahoo.com Cc: FreeSurfer freesurfer@nmr.mgh.harvard.edu Sent: Monday, November 19, 2012 8:57 AM Subject: Re: [Freesurfer] the positions of white/pial surfaces and the brain.mgz
Hi Longchuan
have you tried the -cm (conform to min) option in recon-all?
cheers Bruce
On Sun, 18 Nov 2012, Longchuan Li wrote:
Hi, FreeSurfer experts
I have a question regarding coregistering white and pial surfaces
with the brain.mgz and would appreciate your help on this. I
am working on non-human primates and noticed that my white and pial
surfaces do not have identical positions as brain.mgz. For
example, when I used "mris_fill" to write white and pial surfaces into
volume files, they do not have same sto_xyz and qto_xyz
values as these in the brain.mgz. This is not the case for human
data. So my questions are:
(1) how could I find a transformation matrix between the two, so
that when I am using surface-based tractography in the future,
the program can find the correspondence between the points on the
surfaces and those in the volumetric diffusion MRI data?
(2) How in the future, can I avoid such misregistrations in generating
non-human primate surface files in FreeSurfer?
Thank you very much in advance!
Longchuan
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 and Doug
Thank you very much for the information. I will try this command to register the surfaces with my diffusion volumetric data.
Best Longchuan
________________________________ From: Douglas N Greve greve@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Monday, November 19, 2012 10:43 AM Subject: Re: [Freesurfer] the positions of white/pial surfaces and the brain.mgz
use bbregister, something like bbregister --s subjectname --init-fsl --t2 --mov lowb.nii --reg register.dat where lowb is the low b (usually b=0) volume from your DTI, the one that you used as the template for motion correction. doug
On 11/19/2012 10:30 AM, Bruce Fischl wrote:
Hi Longchuan
yes, I think you can do this with tkregister2. Doug can give you the details Bruce On Mon, 19 Nov 2012, Longchuan Li wrote:
Hi, Bruce
Thank you for the information. I will re-run recon-all using "-cm" option to see if the problem will be solved. In the mean time, do you have any suggestions regarding finding a transformation between the mismatched surfaces and the volume?
Thanks again.
Longchuan
From: Bruce Fischl fischl@nmr.mgh.harvard.edu To: Longchuan Li leonado78@yahoo.com Cc: FreeSurfer freesurfer@nmr.mgh.harvard.edu Sent: Monday, November 19, 2012 8:57 AM Subject: Re: [Freesurfer] the positions of white/pial surfaces and the brain.mgz
Hi Longchuan
have you tried the -cm (conform to min) option in recon-all?
cheers Bruce
On Sun, 18 Nov 2012, Longchuan Li wrote:
Hi, FreeSurfer experts
I have a question regarding coregistering white and pial surfaces
with the brain.mgz and would appreciate your help on this. I
am working on non-human primates and noticed that my white and pial
surfaces do not have identical positions as brain.mgz. For
example, when I used "mris_fill" to write white and pial surfaces into
volume files, they do not have same sto_xyz and qto_xyz
values as these in the brain.mgz. This is not the case for human
data. So my questions are:
(1) how could I find a transformation matrix between the two, so
that when I am using surface-based tractography in the future,
the program can find the correspondence between the points on the
surfaces and those in the volumetric diffusion MRI data?
(2) How in the future, can I avoid such misregistrations in generating
non-human primate surface files in FreeSurfer?
Thank you very much in advance!
Longchuan
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, Doug
I tried bbregister and checked the registration using tkregister2. It seems that this program registers the diffusion image with the anatomical *volume* images in FreeSurfer, such as brain.mgz. My problem is a little unique: I am working on monkey data and I found that my ?h.white surfaces do not have the identical sto_xyz coordinates as those of the anatomical volume images, such as brain.mgz. That is, when I use "mris_fill" to write the ?h.white to a volume file, I find that the center of the images in the header file is not identical to that of the anatomical volume images. In my human data processed using FreeSurfer standard recon-all pipeline, they are identical. Since I am working on monkey data, I used "-notalairach" and "-notal-check" in recon-all to have the piepline work. I suspect this may be related to these options.
So my questions are: (1) what do you think are the reasons causing the inconsistent sto_xyz values between the surface files (?h.white) and voluem files in the non-human data.
(2) Is there any way that I could find a transformation matrix between the ?h.white and my FreeSurfer volume images (such as brain.mgz)?
thank you!
Longchuan
PS: I also used "-cm" option in recon-all as suggested by Bruce. I just got the results and the problem is still there.
________________________________ From: Douglas N Greve greve@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Monday, November 19, 2012 10:43 AM Subject: Re: [Freesurfer] the positions of white/pial surfaces and the brain.mgz
use bbregister, something like bbregister --s subjectname --init-fsl --t2 --mov lowb.nii --reg register.dat where lowb is the low b (usually b=0) volume from your DTI, the one that you used as the template for motion correction. doug
On 11/19/2012 10:30 AM, Bruce Fischl wrote:
Hi Longchuan
yes, I think you can do this with tkregister2. Doug can give you the details Bruce On Mon, 19 Nov 2012, Longchuan Li wrote:
Hi, Bruce
Thank you for the information. I will re-run recon-all using "-cm" option to see if the problem will be solved. In the mean time, do you have any suggestions regarding finding a transformation between the mismatched surfaces and the volume?
Thanks again.
Longchuan
From: Bruce Fischl fischl@nmr.mgh.harvard.edu To: Longchuan Li leonado78@yahoo.com Cc: FreeSurfer freesurfer@nmr.mgh.harvard.edu Sent: Monday, November 19, 2012 8:57 AM Subject: Re: [Freesurfer] the positions of white/pial surfaces and the brain.mgz
Hi Longchuan
have you tried the -cm (conform to min) option in recon-all?
cheers Bruce
On Sun, 18 Nov 2012, Longchuan Li wrote:
Hi, FreeSurfer experts
I have a question regarding coregistering white and pial surfaces
with the brain.mgz and would appreciate your help on this. I
am working on non-human primates and noticed that my white and pial
surfaces do not have identical positions as brain.mgz. For
example, when I used "mris_fill" to write white and pial surfaces into
volume files, they do not have same sto_xyz and qto_xyz
values as these in the brain.mgz. This is not the case for human
data. So my questions are:
(1) how could I find a transformation matrix between the two, so
that when I am using surface-based tractography in the future,
the program can find the correspondence between the points on the
surfaces and those in the volumetric diffusion MRI data?
(2) How in the future, can I avoid such misregistrations in generating
non-human primate surface files in FreeSurfer?
Thank you very much in advance!
Longchuan
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 Longchuan, mris_fill create a volume with a different geometry than orig.mgz (though it is in the same space). What do you want to do exactly? Map the output of mris_fill into the DTI space? The transform from the output of mris_fill to orig.mgz is easy to obtain:
tkregister2 --noedit --mov mris_fill.mgz --s subject --regheader --reg mris_fill.reg.dat
this will be in "register.dat" format/space.
doug
On 11/19/2012 03:35 PM, Longchuan Li wrote:
Hi, Doug
I tried bbregister and checked the registration using tkregister2. It seems that this program registers the diffusion image with the anatomical *volume* images in FreeSurfer, such as brain.mgz. My problem is a little unique: I am working on monkey data and I found that my ?h.white surfaces do not have the identical sto_xyz coordinates as those of the anatomical volume images, such as brain.mgz. That is, when I use "mris_fill" to write the ?h.white to a volume file, I find that the center of the images in the header file is not identical to that of the anatomical volume images. In my human data processed using FreeSurfer standard recon-all pipeline, they are identical. Since I am working on monkey data, I used "-notalairach" and "-notal-check" in recon-all to have the piepline work. I suspect this may be related to these options.
So my questions are: (1) what do you think are the reasons causing the inconsistent sto_xyz values between the surface files (?h.white) and voluem files in the non-human data.
(2) Is there any way that I could find a transformation matrix between the ?h.white and my FreeSurfer volume images (such as brain.mgz)?
thank you!
Longchuan
PS: I also used "-cm" option in recon-all as suggested by Bruce. I just got the results and the problem is still there.
*From:* Douglas N Greve greve@nmr.mgh.harvard.edu *To:* freesurfer@nmr.mgh.harvard.edu *Sent:* Monday, November 19, 2012 10:43 AM *Subject:* Re: [Freesurfer] the positions of white/pial surfaces and the brain.mgz
use bbregister, something like bbregister --s subjectname --init-fsl --t2 --mov lowb.nii --reg register.dat where lowb is the low b (usually b=0) volume from your DTI, the one that you used as the template for motion correction. doug
On 11/19/2012 10:30 AM, Bruce Fischl wrote:
Hi Longchuan
yes, I think you can do this with tkregister2. Doug can give you the details Bruce On Mon, 19 Nov 2012, Longchuan Li wrote:
Hi, Bruce
Thank you for the information. I will re-run recon-all using "-cm" option to see if the problem will be solved. In the mean time, do you have any suggestions regarding finding a transformation between the mismatched surfaces and the volume?
Thanks again.
Longchuan
From: Bruce Fischl <fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu>
To: Longchuan Li <leonado78@yahoo.com mailto:leonado78@yahoo.com> Cc: FreeSurfer <freesurfer@nmr.mgh.harvard.edu
mailto:freesurfer@nmr.mgh.harvard.edu>
Sent: Monday, November 19, 2012 8:57 AM Subject: Re: [Freesurfer] the positions of white/pial surfaces and the brain.mgz
Hi Longchuan
have you tried the -cm (conform to min) option in recon-all?
cheers Bruce
On Sun, 18 Nov 2012, Longchuan Li wrote:
Hi, FreeSurfer experts
I have a question regarding coregistering white and pial surfaces
with the brain.mgz and would appreciate your help on this. I
am working on non-human primates and noticed that my white and pial
surfaces do not have identical positions as brain.mgz. For
example, when I used "mris_fill" to write white and pial surfaces
into
volume files, they do not have same sto_xyz and qto_xyz
values as these in the brain.mgz. This is not the case for human
data. So my questions are:
(1) how could I find a transformation matrix between the two, so
that when I am using surface-based tractography in the future,
the program can find the correspondence between the points on the
surfaces and those in the volumetric diffusion MRI data?
(2) How in the future, can I avoid such misregistrations in
generating
non-human primate surface files in FreeSurfer?
Thank you very much in advance!
Longchuan
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 mailto: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 mailto: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 mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi, Doug
Thank you very much for the information. What I want to do is to use the white and pial surfaces in the FreeSurfer space as the seeds for surface-based tractography implemented in FSL. In order to do that, I need a transformation between the white matter surface and diffusion MR data. For some reason, the space of the white matter surface in my monkey data is not the same as that of the other volumetric data, such as filled.mgz, orig.mgz. This is however not the case for humans, which are processed using the standard FreeSurfer pipeline.
To make things worse, I used "cm" option in recon-all and processed the data in their original resolution(0.5mm isotropic). When I used "mris_fill" without "-c" option, the left and right white volumes will have different dimensions, making it difficult to combine them for registering with filled.mgz. If I use "-c" option, I can combine them since they now have the same dimension. However, they would be "conformed" to 1mm isotropic (originally 0.5m isotropic), which is severely downsampled. I am afraid that this downsampling from 0.5mm to 1mm will affect the registration results. Do you have any suggestions on solving the issue?
I am planning to change the resolution of the image from 0.5mm to 1mm without downsampling before I feed the image to recon-all. I noticed that there are two options in mri_convert (-vs, -cs) that are supposed to be related to this. However, I found both of them downsample the images. Is there any way that I could change the resolution of the images from 0.5mm to 1mm and in the mean time, magnifying the images so that the partial volume effect of the image will not change?
Thank you !
Longchuan
________________________________ From: Douglas N Greve greve@nmr.mgh.harvard.edu To: Longchuan Li leonado78@yahoo.com Cc: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu; Bruce Fischl fischl@nmr.mgh.harvard.edu Sent: Tuesday, November 20, 2012 3:19 PM Subject: Re: [Freesurfer] the positions of white/pial surfaces and the brain.mgz
Hi Longchuan, mris_fill create a volume with a different geometry than orig.mgz (though it is in the same space). What do you want to do exactly? Map the output of mris_fill into the DTI space? The transform from the output of mris_fill to orig.mgz is easy to obtain:
tkregister2 --noedit --mov mris_fill.mgz --s subject --regheader --reg mris_fill.reg.dat
this will be in "register.dat" format/space.
doug
On 11/19/2012 03:35 PM, Longchuan Li wrote:
Hi, Doug
I tried bbregister and checked the registration using tkregister2. It seems that this program registers the diffusion image with the anatomical *volume* images in FreeSurfer, such as brain.mgz. My problem is a little unique: I am working on monkey data and I found that my ?h.white surfaces do not have the identical sto_xyz coordinates as those of the anatomical volume images, such as brain.mgz. That is, when I use "mris_fill" to write the ?h.white to a volume file, I find that the center of the images in the header file is not identical to that of the anatomical volume images. In my human data processed using FreeSurfer standard recon-all pipeline, they are identical. Since I am working on monkey data, I used "-notalairach" and "-notal-check" in recon-all to have the piepline work. I suspect this may be related to these options.
So my questions are: (1) what do you think are the reasons causing the inconsistent sto_xyz values between the surface files (?h.white) and voluem files in the non-human data.
(2) Is there any way that I could find a transformation matrix between the ?h.white and my FreeSurfer volume images (such as brain.mgz)?
thank you!
Longchuan
PS: I also used "-cm" option in recon-all as suggested by Bruce. I just got the results and the problem is still there.
*From:* Douglas N Greve greve@nmr.mgh.harvard.edu *To:* freesurfer@nmr.mgh.harvard.edu *Sent:* Monday, November 19, 2012 10:43 AM *Subject:* Re: [Freesurfer] the positions of white/pial surfaces and the brain.mgz
use bbregister, something like bbregister --s subjectname --init-fsl --t2 --mov lowb.nii --reg register.dat where lowb is the low b (usually b=0) volume from your DTI, the one that you used as the template for motion correction. doug
On 11/19/2012 10:30 AM, Bruce Fischl wrote:
Hi Longchuan
yes, I think you can do this with tkregister2. Doug can give you the details Bruce On Mon, 19 Nov 2012, Longchuan Li wrote:
Hi, Bruce
Thank you for the information. I will re-run recon-all using "-cm" option to see if the problem will be solved. In the mean time, do you have any suggestions regarding finding a transformation between the mismatched surfaces and the volume?
Thanks again.
Longchuan
From: Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> To: Longchuan Li <leonado78@yahoo.com mailto:leonado78@yahoo.com> Cc: FreeSurfer <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu> Sent: Monday, November 19, 2012 8:57 AM Subject: Re: [Freesurfer] the positions of white/pial surfaces and the brain.mgz
Hi Longchuan
have you tried the -cm (conform to min) option in recon-all?
cheers Bruce
On Sun, 18 Nov 2012, Longchuan Li wrote:
Hi, FreeSurfer experts
I have a question regarding coregistering white and pial surfaces
with the brain.mgz and would appreciate your help on this. I
am working on non-human primates and noticed that my white and pial
surfaces do not have identical positions as brain.mgz. For
example, when I used "mris_fill" to write white and pial surfaces into
volume files, they do not have same sto_xyz and qto_xyz
values as these in the brain.mgz. This is not the case for human
data. So my questions are:
(1) how could I find a transformation matrix between the two, so
that when I am using surface-based tractography in the future,
the program can find the correspondence between the points on the
surfaces and those in the volumetric diffusion MRI data?
(2) How in the future, can I avoid such misregistrations in generating
non-human primate surface files in FreeSurfer?
Thank you very much in advance!
Longchuan
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 mailto: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 mailto: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 mailto: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/
Hi Longchuan, I'm still not sure I understand what you are trying to do ultimately. Do you just want a binary map of the surface in the DTI space so that you can use each cortex voxel as a seed? Or do you want to use one of the surface-based ROIs as the seed? This should be possible without re-running recon-all at 1mm. doug
On 11/20/2012 06:01 PM, Longchuan Li wrote:
Hi, Doug
Thank you very much for the information. What I want to do is to use the white and pial surfaces in the FreeSurfer space as the seeds for surface-based tractography implemented in FSL. In order to do that, I need a transformation between the white matter surface and diffusion MR data. For some reason, the space of the white matter surface in my monkey data is not the same as that of the other volumetric data, such as filled.mgz, orig.mgz. This is however not the case for humans, which are processed using the standard FreeSurfer pipeline.
To make things worse, I used "cm" option in recon-all and processed the data in their original resolution(0.5mm isotropic). When I used "mris_fill" without "-c" option, the left and right white volumes will have different dimensions, making it difficult to combine them for registering with filled.mgz. If I use "-c" option, I can combine them since they now have the same dimension. However, they would be "conformed" to 1mm isotropic (originally 0.5m isotropic), which is severely downsampled. I am afraid that this downsampling from 0.5mm to 1mm will affect the registration results. Do you have any suggestions on solving the issue?
I am planning to change the resolution of the image from 0.5mm to 1mm without downsampling before I feed the image to recon-all. I noticed that there are two options in mri_convert (-vs, -cs) that are supposed to be related to this. However, I found both of them downsample the images. Is there any way that I could change the resolution of the images from 0.5mm to 1mm and in the mean time, magnifying the images so that the partial volume effect of the image will not change?
Thank you !
Longchuan
*From:* Douglas N Greve greve@nmr.mgh.harvard.edu *To:* Longchuan Li leonado78@yahoo.com *Cc:* "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu; Bruce Fischl fischl@nmr.mgh.harvard.edu *Sent:* Tuesday, November 20, 2012 3:19 PM *Subject:* Re: [Freesurfer] the positions of white/pial surfaces and the brain.mgz
Hi Longchuan, mris_fill create a volume with a different geometry than orig.mgz (though it is in the same space). What do you want to do exactly? Map the output of mris_fill into the DTI space? The transform from the output of mris_fill to orig.mgz is easy to obtain:
tkregister2 --noedit --mov mris_fill.mgz --s subject --regheader --reg mris_fill.reg.dat
this will be in "register.dat" format/space.
doug
On 11/19/2012 03:35 PM, Longchuan Li wrote:
Hi, Doug
I tried bbregister and checked the registration using tkregister2.
It seems that this program registers the diffusion image with the anatomical *volume* images in FreeSurfer, such as brain.mgz. My problem is a little unique: I am working on monkey data and I found that my ?h.white surfaces do not have the identical sto_xyz coordinates as those of the anatomical volume images, such as brain.mgz. That is, when I use "mris_fill" to write the ?h.white to a volume file, I find that the center of the images in the header file is not identical to that of the anatomical volume images. In my human data processed using FreeSurfer standard recon-all pipeline, they are identical. Since I am working on monkey data, I used "-notalairach" and "-notal-check" in recon-all to have the piepline work. I suspect this may be related to these options.
So my questions are: (1) what do you think are the reasons causing the inconsistent
sto_xyz values between the surface files (?h.white) and voluem files in the non-human data.
(2) Is there any way that I could find a transformation matrix
between the ?h.white and my FreeSurfer volume images (such as brain.mgz)?
thank you!
Longchuan
PS: I also used "-cm" option in recon-all as suggested by Bruce. I
just got the results and the problem is still there.
*From:* Douglas N Greve <greve@nmr.mgh.harvard.edu
mailto:greve@nmr.mgh.harvard.edu>
*To:* freesurfer@nmr.mgh.harvard.edu
mailto:freesurfer@nmr.mgh.harvard.edu
*Sent:* Monday, November 19, 2012 10:43 AM *Subject:* Re: [Freesurfer] the positions of white/pial surfaces and
the brain.mgz
use bbregister, something like bbregister --s subjectname --init-fsl --t2 --mov lowb.nii --reg
register.dat
where lowb is the low b (usually b=0) volume from your DTI, the one that you used as the template for motion correction. doug
On 11/19/2012 10:30 AM, Bruce Fischl wrote:
Hi Longchuan
yes, I think you can do this with tkregister2. Doug can give you the details Bruce On Mon, 19 Nov 2012, Longchuan Li wrote:
Hi, Bruce
Thank you for the information. I will re-run recon-all using "-cm" option to see if the problem will be solved. In the mean time, do you have any suggestions regarding finding a transformation between the mismatched surfaces and the volume?
Thanks again.
Longchuan
From: Bruce Fischl <fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu>>
To: Longchuan Li <leonado78@yahoo.com
mailto:leonado78@yahoo.com <mailto:leonado78@yahoo.com mailto:leonado78@yahoo.com>>
Cc: FreeSurfer <freesurfer@nmr.mgh.harvard.edu
mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu>>
Sent: Monday, November 19, 2012 8:57 AM Subject: Re: [Freesurfer] the positions of white/pial surfaces
and the
brain.mgz
Hi Longchuan
have you tried the -cm (conform to min) option in recon-all?
cheers Bruce
On Sun, 18 Nov 2012, Longchuan Li wrote:
Hi, FreeSurfer experts
I have a question regarding coregistering white and pial surfaces
with the brain.mgz and would appreciate your help on this. I
am working on non-human primates and noticed that my white and pial
surfaces do not have identical positions as brain.mgz. For
example, when I used "mris_fill" to write white and pial
surfaces into
volume files, they do not have same sto_xyz and qto_xyz
values as these in the brain.mgz. This is not the case for human
data. So my questions are:
(1) how could I find a transformation matrix between the two, so
that when I am using surface-based tractography in the future,
the program can find the correspondence between the points on the
surfaces and those in the volumetric diffusion MRI data?
(2) How in the future, can I avoid such misregistrations in
generating
non-human primate surface files in FreeSurfer?
Thank you very much in advance!
Longchuan
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
mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu mailto: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 mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu mailto: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
mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu mailto: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 mailto: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/
Hi, Doug
Thank you for following up the issue. I think that I have solved the problem. What I wanted was to derive a binary map of the surface in the DTI space so that each cortex voxel can be used as a seed.
Thank you very much for the help! Longchuan
________________________________ From: Douglas N Greve greve@nmr.mgh.harvard.edu To: Longchuan Li leonado78@yahoo.com Cc: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, November 21, 2012 3:20 PM Subject: Re: [Freesurfer] the positions of white/pial surfaces and the brain.mgz
Hi Longchuan, I'm still not sure I understand what you are trying to do ultimately. Do you just want a binary map of the surface in the DTI space so that you can use each cortex voxel as a seed? Or do you want to use one of the surface-based ROIs as the seed? This should be possible without re-running recon-all at 1mm. doug
On 11/20/2012 06:01 PM, Longchuan Li wrote:
Hi, Doug
Thank you very much for the information. What I want to do is to use the white and pial surfaces in the FreeSurfer space as the seeds for surface-based tractography implemented in FSL. In order to do that, I need a transformation between the white matter surface and diffusion MR data. For some reason, the space of the white matter surface in my monkey data is not the same as that of the other volumetric data, such as filled.mgz, orig.mgz. This is however not the case for humans, which are processed using the standard FreeSurfer pipeline.
To make things worse, I used "cm" option in recon-all and processed the data in their original resolution(0.5mm isotropic). When I used "mris_fill" without "-c" option, the left and right white volumes will have different dimensions, making it difficult to combine them for registering with filled.mgz. If I use "-c" option, I can combine them since they now have the same dimension. However, they would be "conformed" to 1mm isotropic (originally 0.5m isotropic), which is severely downsampled. I am afraid that this downsampling from 0.5mm to 1mm will affect the registration results. Do you have any suggestions on solving the issue?
I am planning to change the resolution of the image from 0.5mm to 1mm without downsampling before I feed the image to recon-all. I noticed that there are two options in mri_convert (-vs, -cs) that are supposed to be related to this. However, I found both of them downsample the images. Is there any way that I could change the resolution of the images from 0.5mm to 1mm and in the mean time, magnifying the images so that the partial volume effect of the image will not change?
Thank you !
Longchuan
*From:* Douglas N Greve greve@nmr.mgh.harvard.edu *To:* Longchuan Li leonado78@yahoo.com *Cc:* "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu; Bruce Fischl fischl@nmr.mgh.harvard.edu *Sent:* Tuesday, November 20, 2012 3:19 PM *Subject:* Re: [Freesurfer] the positions of white/pial surfaces and the brain.mgz
Hi Longchuan, mris_fill create a volume with a different geometry than orig.mgz (though it is in the same space). What do you want to do exactly? Map the output of mris_fill into the DTI space? The transform from the output of mris_fill to orig.mgz is easy to obtain:
tkregister2 --noedit --mov mris_fill.mgz --s subject --regheader --reg mris_fill.reg.dat
this will be in "register.dat" format/space.
doug
On 11/19/2012 03:35 PM, Longchuan Li wrote:
Hi, Doug
I tried bbregister and checked the registration using tkregister2.
It seems that this program registers the diffusion image with the anatomical *volume* images in FreeSurfer, such as brain.mgz. My problem is a little unique: I am working on monkey data and I found that my ?h.white surfaces do not have the identical sto_xyz coordinates as those of the anatomical volume images, such as brain.mgz. That is, when I use "mris_fill" to write the ?h.white to a volume file, I find that the center of the images in the header file is not identical to that of the anatomical volume images. In my human data processed using FreeSurfer standard recon-all pipeline, they are identical. Since I am working on monkey data, I used "-notalairach" and "-notal-check" in recon-all to have the piepline work. I suspect this may be related to these options.
So my questions are: (1) what do you think are the reasons causing the inconsistent
sto_xyz values between the surface files (?h.white) and voluem files in the non-human data.
(2) Is there any way that I could find a transformation matrix
between the ?h.white and my FreeSurfer volume images (such as brain.mgz)?
thank you!
Longchuan
PS: I also used "-cm" option in recon-all as suggested by Bruce. I
just got the results and the problem is still there.
*From:* Douglas N Greve <greve@nmr.mgh.harvard.edu
mailto:greve@nmr.mgh.harvard.edu>
*To:* freesurfer@nmr.mgh.harvard.edu
mailto:freesurfer@nmr.mgh.harvard.edu
*Sent:* Monday, November 19, 2012 10:43 AM *Subject:* Re: [Freesurfer] the positions of white/pial surfaces and
the brain.mgz
use bbregister, something like bbregister --s subjectname --init-fsl --t2 --mov lowb.nii --reg
register.dat
where lowb is the low b (usually b=0) volume from your DTI, the one that you used as the template for motion correction. doug
On 11/19/2012 10:30 AM, Bruce Fischl wrote:
Hi Longchuan
yes, I think you can do this with tkregister2. Doug can give you the details Bruce On Mon, 19 Nov 2012, Longchuan Li wrote:
Hi, Bruce
Thank you for the information. I will re-run recon-all using "-cm" option to see if the problem will be solved. In the mean time, do you have any suggestions regarding finding a transformation between the mismatched surfaces and the volume?
Thanks again.
Longchuan
From: Bruce Fischl <fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu>>
To: Longchuan Li <leonado78@yahoo.com
mailto:leonado78@yahoo.com <mailto:leonado78@yahoo.com mailto:leonado78@yahoo.com>>
Cc: FreeSurfer <freesurfer@nmr.mgh.harvard.edu
mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu>>
Sent: Monday, November 19, 2012 8:57 AM Subject: Re: [Freesurfer] the positions of white/pial surfaces
and the
brain.mgz
Hi Longchuan
have you tried the -cm (conform to min) option in recon-all?
cheers Bruce
On Sun, 18 Nov 2012, Longchuan Li wrote:
Hi, FreeSurfer experts
I have a question regarding coregistering white and pial surfaces
with the brain.mgz and would appreciate your help on this. I
am working on non-human primates and noticed that my white and pial
surfaces do not have identical positions as brain.mgz. For
example, when I used "mris_fill" to write white and pial
surfaces into
volume files, they do not have same sto_xyz and qto_xyz
values as these in the brain.mgz. This is not the case for human
data. So my questions are:
(1) how could I find a transformation matrix between the two, so
that when I am using surface-based tractography in the future,
the program can find the correspondence between the points on the
surfaces and those in the volumetric diffusion MRI data?
(2) How in the future, can I avoid such misregistrations in
generating
non-human primate surface files in FreeSurfer?
Thank you very much in advance!
Longchuan
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
mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu mailto: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 mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu mailto: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
mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu mailto: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 mailto: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@nmr.mgh.harvard.edu
-
Bruce Fischl -
Douglas N Greve -
Longchuan Li