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 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.
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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, 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 fischl@nmr.mgh.harvard.edu To: Longchuan Li leonado78@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 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.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
yes, I have it On Tue, 19 Mar 2013, Longchuan Li wrote:
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 fischl@nmr.mgh.harvard.edu To: Longchuan Li leonado78@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 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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Longchuan Li