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
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
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 fischl@nmr.mgh.harvard.edu To: Longchuan Li leonado78@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.
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 fischl@nmr.mgh.harvard.edu To: Longchuan Li leonado78@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.
We use the MNI305through the (affine) talairach.xfm transform. doug On 03/17/2013 11:47 AM, Bruce Fischl wrote:
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 fischl@nmr.mgh.harvard.edu To: Longchuan Li leonado78@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
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 fischl@nmr.mgh.harvard.edu To: Longchuan Li leonado78@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 fischl@nmr.mgh.harvard.edu To: Longchuan Li leonado78@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.
For many non-human primate species, volume templates already exist. I would recommend using them and aligning your surface templates to them to aid in the ability to compare studies across laboratories in the same space.
For rhesus, see the 112RM-SL atlas.
Best Regards, Donald McLaren ================= D.G. McLaren, Ph.D. Research Fellow, Department of Neurology, Massachusetts General Hospital and Harvard Medical School Postdoctoral Research Fellow, GRECC, Bedford VA Website: http://www.martinos.org/~mclaren Office: (773) 406-2464 ===================== This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is intended only for the use of the individual or entity named above. If the reader of the e-mail is not the intended recipient or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that you are in possession of confidential and privileged information. Any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited and may be unlawful. If you have received this e-mail unintentionally, please immediately notify the sender via telephone at (773) 406-2464 or email.
On Fri, Mar 15, 2013 at 4:41 PM, Longchuan Li leonado78@yahoo.com 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
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
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Bruce Fischl -
Douglas N Greve -
Longchuan Li -
MCLAREN, Donald