I am wondering why you didn't tell them to go through fsvarege space? I thought that was an easy way to go from SPM MNI to freesurfer land.
tksurfer fsaverage lh inflated -aparc -mni152reg -overlay /pathname/to/spm/roi/yourfile.img
I am wondering because when I look at the segmentation for fsaverage, it seems like it is missing a lot of the gray matter, particularly in the big sulci, most likely from the 'smoothing' that comes with averaging subjects together. And therefore I wonder if this is the best thing to use as an intermediate step. Are you instead suggesting (as it seemed like in this thread), to put the SPM roi into individual subject space and then somehow project it to the surface in free surfer?
Thanks, Stephanie
+++++++++++++++++++++++++
Stephanie McMains Neuroimaging Staff Scientist Center for Brain Science Harvard University 52 Oxford Street Cambridge, MA 02138
+++++++++++++++++++++++++ For answers to frequently asked questions: http://cbs.fas.harvard.edu/science/core-facilities/neuroimaging/information-...
Hi Stephanie, I don't know which recommendation you are referring to. We get a lot of emails, and I can't remember each one. Can you repost with the full thread? doug
On 06/06/2013 10:40 AM, McMains, Stephanie wrote:
I am wondering why you didn't tell them to go through fsvarege space? I thought that was an easy way to go from SPM MNI to freesurfer land.
/tksurfer fsaverage lh inflated -aparc -mni152reg -overlay /pathname/to/spm/roi/yourfile.img/
I am wondering because when I look at the segmentation for fsaverage, it seems like it is missing a lot of the gray matter, particularly in the big sulci, most likely from the 'smoothing' that comes with averaging subjects together. And therefore I wonder if this is the best thing to use as an intermediate step. Are you instead suggesting (as it seemed like in this thread), to put the SPM roi into individual subject space and then somehow project it to the surface in free surfer?
Thanks, Stephanie
+++++++++++++++++++++++++
Stephanie McMains Neuroimaging Staff Scientist Center for Brain Science Harvard University 52 Oxford Street Cambridge, MA 02138
+++++++++++++++++++++++++ For answers to frequently asked questions: http://cbs.fas.harvard.edu/science/core-facilities/neuroimaging/information-...
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi doug Thank you for giving this information, I used the command: "/tksurfer fsaverage lh inflated -aparc -mni152reg -overlay /pathname/to/spm/roi/yourfile.img/", but do not have results for me, and do not know how to do next? thanks!
Bo
At 2013-06-06 23:04:30,"Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
Hi Stephanie, I don't know which recommendation you are referring to. We get a lot of emails, and I can't remember each one. Can you repost with the full thread? doug
On 06/06/2013 10:40 AM, McMains, Stephanie wrote:
I am wondering why you didn't tell them to go through fsvarege space? I thought that was an easy way to go from SPM MNI to freesurfer land.
/tksurfer fsaverage lh inflated -aparc -mni152reg -overlay /pathname/to/spm/roi/yourfile.img/
I am wondering because when I look at the segmentation for fsaverage, it seems like it is missing a lot of the gray matter, particularly in the big sulci, most likely from the 'smoothing' that comes with averaging subjects together. And therefore I wonder if this is the best thing to use as an intermediate step. Are you instead suggesting (as it seemed like in this thread), to put the SPM roi into individual subject space and then somehow project it to the surface in free surfer?
Thanks, Stephanie
+++++++++++++++++++++++++
Stephanie McMains Neuroimaging Staff Scientist Center for Brain Science Harvard University 52 Oxford Street Cambridge, MA 02138
+++++++++++++++++++++++++ For answers to frequently asked questions: http://cbs.fas.harvard.edu/science/core-facilities/neuroimaging/information-...
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 greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 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
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 Bo,
tksurfer doesn't take a path to a file. Read the help on it - you need to reconstrcut the subject with recon-all then give it the subject id. To project a volumetric map onto the surface use mri_vol2surf, with the registration typically computed by bbregister.
cheers Bruce
On Mon, 17 Jun 2013, xiangbo_2010 wrote:
Hi dougThank you for giving this information, I used the
command: "/tksurfer fsaverage lh inflated -aparc -mni152reg -overlay /pathname/to/s
pm/roi/yourfile.img/", but do not have results for me, and do not know how to do next? thanks!
Bo
At 2013-06-06 23:04:30,"Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
Hi Stephanie, I don't know which recommendation you are referring to. We get a lot of emails, and I can't remember each one. Can you repost with the full thread? doug
On 06/06/2013 10:40 AM, McMains, Stephanie wrote:
I am wondering why you didn't tell them to go through fsvarege space? I thought that was an easy way to go from SPM MNI to freesurfer land.
/tksurfer fsaverage lh inflated -aparc -mni152reg -overlay /pathname/to/
spm/roi/yourfile.img/
I am wondering because when I look at the segmentation for fsaverage, it seems like it is missing a lot of the gray matter, particularly in the big sulci, most likely from the 'smoothing' that comes with averaging subjects together. And therefore I wonder if this is the best thing to use as an intermediate step. Are you instead suggesting (as it seemed like in this thread), to put the SPM roi into individual subject space and then somehow project it to the surface in free surfer?
Thanks, Stephanie
+++++++++++++++++++++++++
Stephanie McMains Neuroimaging Staff Scientist Center for Brain Science Harvard University 52 Oxford Street Cambridge, MA 02138
+++++++++++++++++++++++++ For answers to frequently asked questions: http://cbs.fas.harvard.edu/science/core-facilities/neuroimaging/informati
on-investigators/faq
_______________________________________________ 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 greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 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
The information in this e-mail is intended only for the person to whom it i
s
addressed. If you believe this e-mail was sent to you in error and the e-ma
il
contains patient information, please contact the Partners Compliance HelpLi
ne at
http://www.partners.org/complianceline%C2%A0.%C2%A0If%C2%A0the%C2%A0e-mail%C...
rror
but does not contain patient information, please contact the sender and pro
perly
dispose of the e-mail.
Hi Bruce
Thank you for my help, when I use the bbregister, do not know how to choose data for --mov, thanks!
Bo
At 2013-06-17 20:34:39,"Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
Hi Bo,
tksurfer doesn't take a path to a file. Read the help on it - you need to reconstrcut the subject with recon-all then give it the subject id. To project a volumetric map onto the surface use mri_vol2surf, with the registration typically computed by bbregister.
cheers Bruce
On Mon, 17 Jun 2013, xiangbo_2010 wrote:
Hi dougThank you for giving this information, I used the
command: "/tksurfer fsaverage lh inflated -aparc -mni152reg -overlay /pathname/to/s
pm/roi/yourfile.img/", but do not have results for me, and do not know how to do next? thanks!
Bo
At 2013-06-06 23:04:30,"Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
Hi Stephanie, I don't know which recommendation you are referring to. We get a lot of emails, and I can't remember each one. Can you repost with the full thread? doug
On 06/06/2013 10:40 AM, McMains, Stephanie wrote:
I am wondering why you didn't tell them to go through fsvarege space? I thought that was an easy way to go from SPM MNI to freesurfer land.
/tksurfer fsaverage lh inflated -aparc -mni152reg -overlay /pathname/to/
spm/roi/yourfile.img/
I am wondering because when I look at the segmentation for fsaverage, it seems like it is missing a lot of the gray matter, particularly in the big sulci, most likely from the 'smoothing' that comes with averaging subjects together. And therefore I wonder if this is the best thing to use as an intermediate step. Are you instead suggesting (as it seemed like in this thread), to put the SPM roi into individual subject space and then somehow project it to the surface in free surfer?
Thanks, Stephanie
+++++++++++++++++++++++++
Stephanie McMains Neuroimaging Staff Scientist Center for Brain Science Harvard University 52 Oxford Street Cambridge, MA 02138
+++++++++++++++++++++++++ For answers to frequently asked questions: http://cbs.fas.harvard.edu/science/core-facilities/neuroimaging/informati
on-investigators/faq
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 greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 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
The information in this e-mail is intended only for the person to whom it i
s
addressed. If you believe this e-mail was sent to you in error and the e-ma
il
contains patient information, please contact the Partners Compliance HelpLi
ne at
http://www.partners.org/complianceline . If the e-mail was sent to you in e
rror
but does not contain patient information, please contact the sender and pro
perly
dispose of the e-mail.
what are you trying to map to the surface? On Mon, 17 Jun 2013, xiangbo_2010 wrote:
Hi Bruce Thank you for my help, when I use the bbregister, do not know how to choose data for --mov, thanks!
Bo
At 2013-06-17 20:34:39,"Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
Hi Bo,
tksurfer doesn't take a path to a file. Read the help on it - you need to reconstrcut the subject with recon-all then give it the subject id. To project a volumetric map onto the surface use mri_vol2surf, with the registration typically computed by bbregister.
cheers Bruce
On Mon, 17 Jun 2013, xiangbo_2010 wrote:
Hi dougThank you for giving this information, I used the
command: "/tksurfer fsaverage lh inflated -aparc -mni152reg -overlay /pathn
ame/to/s
pm/roi/yourfile.img/", but do not have results for me, and do not know ho
w
to do next? thanks! Bo At 2013-06-06 23:04:30,"Douglas N Greve" greve@nmr.mgh.harvard.edu wrot
e:
>Hi Stephanie, I don't know which recommendation you are referring to. We
>get a lot of emails, and I can't remember each one. Can you repost with >the full thread? >doug > > >On 06/06/2013 10:40 AM, McMains, Stephanie wrote: >> I am wondering why you didn't tell them to go through fsvarege space? >> I thought that was an easy way to go from SPM MNI to freesurfer land. >> >>> /tksurfer fsaverage lh inflated -aparc -mni152reg -overlay /pathname/
to/
spm/roi/yourfile.img/ >> >> >> I am wondering because when I look at the segmentation for fsaverage, >> it seems like it is missing a lot of the gray matter, particularly in >> the big sulci, most likely from the 'smoothing' that comes with >> averaging subjects together. And therefore I wonder if this is the >> best thing to use as an intermediate step. Are you instead suggesting
>> (as it seemed like in this thread), to put the SPM roi into individual
>> subject space and then somehow project it to the surface in free surfe
r?
>> >> Thanks, >> Stephanie >> >> >> +++++++++++++++++++++++++ >> >> Stephanie McMains >> Neuroimaging Staff Scientist >> Center for Brain Science >> Harvard University >> 52 Oxford Street >> Cambridge, MA 02138 >> >> +++++++++++++++++++++++++ >> For answers to frequently asked questions: >> http://cbs.fas.harvard.edu/science/core-facilities/neuroimaging/inform
ati
on-investigators/faq >> >> >> >> >> >> >> >> >> >> _______________________________________________ >> 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 >greve@nmr.mgh.harvard.edu >Phone Number: 617-724-2358 >Fax: 617-726-7422 > >Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >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 > > >The information in this e-mail is intended only for the person to whom i
t i
s >addressed. If you believe this e-mail was sent to you in error and the e
-ma
il >contains patient information, please contact the Partners Compliance Hel
pLi
ne at >http://www.partners.org/complianceline%C2%A0.%C2%A0If%C2%A0the%C2%A0e-mail%C...
n e
rror >but does not contain patient information, please contact the sender and
pro
perly >dispose of the e-mail. >
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Douglas N Greve -
McMains, Stephanie -
xiangbo_2010