[Freesurfer] Visualize cortical projections of fiber pathways using FreeSurfer
Hi, FreeSurfer experts I have a question regarding visualizing the cortical projections of a fiber bundle using FreeSurfer based on the data from a group of subjects. Since I am interested in seeing both the cortical projections on the surface and the trajectory of the fiber bundle derived from the group, I would like to have them in the same space. I wonder wether fsaverage surface template and mni305.cor.mgz have such a spatial correspondence. What I am planning to do: To show the cortical projections of the fiber pathways: (1) derive the fiber pathways using FSL (2) map the transformations between each subject's T1w image to mni305 (or any templates in FS that have spatial correspondence with fsaverage surface template) using non-linear methods, such as fnirt. (3) transform the fiber pathway from each subject's space to the mni305 space using the transformations derived earlier. (4) sample the projections to the surface using mri_vol2surf In this way, I will also have the volume average of the fiber pathways to show the trajectories of the fiber pathway. Do these steps sound ok? Is there any better way to do what I want to achieve here? Many thanks in advance! Longchuan___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] make a volume template from the surface-based template for non-human primates
Hi, Bruce The command line I used is: mris_fill -r 1 -c rh.white rh.white.nii.gz I attached the rh.white in my previous mail. Could you see it in the attachment? Thank you! Longchuan From: Bruce Fischl fis...@nmr.mgh.harvard.edu To: Longchuan Li leonad...@yahoo.com Cc: FreeSurfer freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, March 19, 2013 8:10 PM Subject: Re: [Freesurfer] make a volume template from the surface-based template for non-human primates can you send your mris_fill command line? And maybe the lh.white surface you are trying to fill? Bruce On Tue, 19 Mar 2013, Longchuan Li wrote: Hi, Bruce This is the lh.white that gives me the empty volume when I use mris_fill to sample it to the volume space. Could you help diagnose what is causing it? Thank you very much in advance! Lognchuan From: Bruce Fischl fis...@nmr.mgh.harvard.edu To: Longchuan Li leonad...@yahoo.com Cc: FreeSurfer freesurfer@nmr.mgh.harvard.edu Sent: Sunday, March 17, 2013 11:47 AM Subject: Re: [Freesurfer] make a volume template from the surface-based template for non-human primates Hi Longchuan I'm not sure what space the volume average is constructed in - Doug would know. Probably talairach, in which case it won't match the surfaces well. Can you send along your mris_fill command line? It shouldn't produce an empty volume. There's no reason to look at the inflated surfaces in the volume though - they have no volumetric meaning. cheers Bruce On Fri, 15 Mar 2013, Longchuan Li wrote: Hi, Bruce Sorry for the late reply as I was trying to figure it out by myself. I mean the average of the subjects in the volume space that were used for generating the surface template. Actually I kind of found a volume average in the mri folder named as T1.mgz that seems to correspond to the surface template for the non-human primates. Perhaps because my ?h.white and ?.pial surface files do not have the identical origins as that of the volume template, when I used the function mri_surf2vol to project the mgh surface file to the volume average, I always got the outputs telling me there is 0 hits. I tried to diagnose it by projecting the ?h.white and ?h.pial to the volume using mri_fill and I got an empty volume. I then tried to project ?h.inflated to the volume space using the mri_fill and this time, I got a mask in the output volume space. Therefore, i suspect that there is a mismatch of the origins between the ?h.white and the volume template in the mri folder. Could you please show me what are the best strategies to correctly project the mgh file to the volume template in the 'mri' folder? Many thanks Longchuan ___ _ From: Bruce Fischl fis...@nmr.mgh.harvard.edu To: Longchuan Li leonad...@yahoo.com Cc: FreeSurfer freesurfer@nmr.mgh.harvard.edu Sent: Friday, March 15, 2013 4:56 PM Subject: Re: [Freesurfer] make a volume template from the surface-based template for non-human primates Hi Longchuan what kind of volume template do you mean? Bruce On Fri, 15 Mar 2013, Longchuan Li wrote: Hi, FreeSurfer experts I have a question regarding making a volume template based on the surface template for non-human primates. I have made a surface template using a group of monkeys and now, we want to see the result, which is a mgh surface file, on the coronal slices of the template. So I am planning to generate a volume template corresponding to the surface template and then project the mgh file to the volume for viewing. Could someone tell me what is the best way to generate such a volume template? Many thanks 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 The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail
Re: [Freesurfer] make a volume template from the surface-based template for non-human primates
Hi, Bruce Thank you for the information. I tried all possible combinations of mris_fill command line and none of them worked. Also, I loaded my ?h.white in tksurfer and confirmed that the surface is there. Do you want me to send you the surface file? One example I used is this: mris_fill -c -r 1 lh.white lh.white.nii.gz Thanks Longchuan From: Bruce Fischl fis...@nmr.mgh.harvard.edu To: Longchuan Li leonad...@yahoo.com Cc: FreeSurfer freesurfer@nmr.mgh.harvard.edu Sent: Sunday, March 17, 2013 11:47 AM Subject: Re: [Freesurfer] make a volume template from the surface-based template for non-human primates Hi Longchuan I'm not sure what space the volume average is constructed in - Doug would know. Probably talairach, in which case it won't match the surfaces well. Can you send along your mris_fill command line? It shouldn't produce an empty volume. There's no reason to look at the inflated surfaces in the volume though - they have no volumetric meaning. cheers Bruce On Fri, 15 Mar 2013, Longchuan Li wrote: Hi, Bruce Sorry for the late reply as I was trying to figure it out by myself. I mean the average of the subjects in the volume space that were used for generating the surface template. Actually I kind of found a volume average in the mri folder named as T1.mgz that seems to correspond to the surface template for the non-human primates. Perhaps because my ?h.white and ?.pial surface files do not have the identical origins as that of the volume template, when I used the function mri_surf2vol to project the mgh surface file to the volume average, I always got the outputs telling me there is 0 hits. I tried to diagnose it by projecting the ?h.white and ?h.pial to the volume using mri_fill and I got an empty volume. I then tried to project ?h.inflated to the volume space using the mri_fill and this time, I got a mask in the output volume space. Therefore, i suspect that there is a mismatch of the origins between the ?h.white and the volume template in the mri folder. Could you please show me what are the best strategies to correctly project the mgh file to the volume template in the 'mri' folder? Many thanks Longchuan From: Bruce Fischl fis...@nmr.mgh.harvard.edu To: Longchuan Li leonad...@yahoo.com Cc: FreeSurfer freesurfer@nmr.mgh.harvard.edu Sent: Friday, March 15, 2013 4:56 PM Subject: Re: [Freesurfer] make a volume template from the surface-based template for non-human primates Hi Longchuan what kind of volume template do you mean? Bruce On Fri, 15 Mar 2013, Longchuan Li wrote: Hi, FreeSurfer experts I have a question regarding making a volume template based on the surface template for non-human primates. I have made a surface template using a group of monkeys and now, we want to see the result, which is a mgh surface file, on the coronal slices of the template. So I am planning to generate a volume template corresponding to the surface template and then project the mgh file to the volume for viewing. Could someone tell me what is the best way to generate such a volume template? Many thanks 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 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 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] make a volume template from the surface-based template for non-human primates
Hi, FreeSurfer experts I have a question regarding making a volume template based on the surface template for non-human primates. I have made a surface template using a group of monkeys and now, we want to see the result, which is a mgh surface file, on the coronal slices of the template. So I am planning to generate a volume template corresponding to the surface template and then project the mgh file to the volume for viewing. Could someone tell me what is the best way to generate such a volume template? Many thanks in advance! Longchuan___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] make a volume template from the surface-based template for non-human primates
Hi, Bruce Sorry for the late reply as I was trying to figure it out by myself. I mean the average of the subjects in the volume space that were used for generating the surface template. Actually I kind of found a volume average in the mri folder named as T1.mgz that seems to correspond to the surface template for the non-human primates. Perhaps because my ?h.white and ?.pial surface files do not have the identical origins as that of the volume template, when I used the function mri_surf2vol to project the mgh surface file to the volume average, I always got the outputs telling me there is 0 hits. I tried to diagnose it by projecting the ?h.white and ?h.pial to the volume using mri_fill and I got an empty volume. I then tried to project ?h.inflated to the volume space using the mri_fill and this time, I got a mask in the output volume space. Therefore, i suspect that there is a mismatch of the origins between the ?h.white and the volume template in the mri folder. Could you please show me what are the best strategies to correctly project the mgh file to the volume template in the 'mri' folder? Many thanks Longchuan From: Bruce Fischl fis...@nmr.mgh.harvard.edu To: Longchuan Li leonad...@yahoo.com Cc: FreeSurfer freesurfer@nmr.mgh.harvard.edu Sent: Friday, March 15, 2013 4:56 PM Subject: Re: [Freesurfer] make a volume template from the surface-based template for non-human primates Hi Longchuan what kind of volume template do you mean? Bruce On Fri, 15 Mar 2013, Longchuan Li wrote: Hi, FreeSurfer experts I have a question regarding making a volume template based on the surface template for non-human primates. I have made a surface template using a group of monkeys and now, we want to see the result, which is a mgh surface file, on the coronal slices of the template. So I am planning to generate a volume template corresponding to the surface template and then project the mgh file to the volume for viewing. Could someone tell me what is the best way to generate such a volume template? Many thanks 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 The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] the positions of white/pial surfaces and the brain.mgz
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 gr...@nmr.mgh.harvard.edu To: Longchuan Li leonad...@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 gr...@nmr.mgh.harvard.edu *To:* Longchuan Li leonad...@yahoo.com *Cc:* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu; Bruce Fischl fis...@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
Re: [Freesurfer] the positions of white/pial surfaces and the brain.mgz
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 gr...@nmr.mgh.harvard.edu To: Longchuan Li leonad...@yahoo.com Cc: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu; Bruce Fischl fis...@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 gr...@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
Re: [Freesurfer] the positions of white/pial surfaces and the brain.mgz
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 fis...@nmr.mgh.harvard.edu To: Longchuan Li leonad...@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 The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] the positions of white/pial surfaces and the brain.mgz
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 gr...@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 fis...@nmr.mgh.harvard.edu To: Longchuan Li leonad...@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 -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html 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___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] the positions of white/pial surfaces and the brain.mgz
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 gr...@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 fis...@nmr.mgh.harvard.edu To: Longchuan Li leonad...@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 -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html 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___ 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
[Freesurfer] the positions of white/pial surfaces and the brain.mgz
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___ 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] The mismatched color in the tksurfer color bar for surface file
Hi, Doug and other FreeSurfer experts: I noticed that the color in a surface file I generated (*.mgh with the values ranging from 0 to 1) does not match that in the color bar. For example, the lowest value in the surface file has much darker red hue than the lowest values in the color bar (bright red). Is there any remedy for this mismatch? Also, I intended to attach an image in the email, but was told that the email contains blocked images. Thank you in advance! Longchuan___ 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] transfer label from high-resolution mesh to low resolution mesh
Hi, all I am trying to transfer some labels on a high-resolution white surface mesh (~100K) to a corresponding low-resolution white mesh(~10K) that is generated using FS function mris_decimate. Could someone tell me what is the most efficient way to realize that? Many thanks in advance! Longchuan___ 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] A question about downsmapling mulitple surfaces (white, pial, sphere) for registration
Hi, FreeSurfer experts Currently, I am planning to run tractography using wm surfaces as seed masks and pial surfaces as stop masks implemented in FSL. In order to make fibers go through one hemisphere to another, I need to remove the medial wall from both seed surfaces and the pial surfaces. However, as the original surfaces' resolution is too high, I will need to downsample the surfaces first, in order to manage the computational time to a reasonable time limit. My strategy is like this: (1) downasample the sphere, pial and white from original 700K to 10K using mris_decimate with a factor of 0.1 (2) register the subject's downsampled sphere to the template surface sphere (3) transfer the label file with medial wall excluded from the template space to the subject's sphere space based on the warping file. (4) convert the label file to seed mask (based on white surface) and stop mask (based on pial surface). using a FSL tool My questions are: (1) Can surface-based registration be properly done when I used the downsampled version of the sphere to register to the template's sphere? (2) As my pial, sphere and white surfaces are downsampled separately by repeatedly using the mris_decimate, will they still have that point-to-point correspondence as the original ones? I would appreciate if anyone could help on this and point out any potential problems and/or better strategies Longchuan ___ 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.
