Re: [Freesurfer] make a volume template from the surface-based template for non-human primates
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 To: Longchuan Li Cc: FreeSurfer 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 > To: Longchuan Li > Cc: FreeSurfer > 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 > > To: Longchuan Li > > Cc: FreeSurfer > > 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 n
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 To: Longchuan Li Cc: FreeSurfer 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 > To: Longchuan Li > Cc: FreeSurfer > 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 > > To: Longchuan Li > > Cc: FreeSurfer > > 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
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 To: Longchuan Li Cc: FreeSurfer 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 > To: Longchuan Li > Cc: FreeSurfer > 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.
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 To: Longchuan Li Cc: FreeSurfer 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 > To: Longchuan Li > Cc: FreeSurfer > 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.
Re: [Freesurfer] make a volume template from the surface-based template for non-human primates
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 >> To: Longchuan Li >> Cc: FreeSurfer >> 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 -- 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
Re: [Freesurfer] make a volume template from the surface-based template for non-human primates
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 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 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 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 To: Longchuan Li Cc: FreeSurfer 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 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 To: Longchuan Li Cc: FreeSurfer 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 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 > > > ___ 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.
