External Email - Use Caution
Hello,
I am using mri_vol2surf to project my volume maps on to the surface. There is a dACC/insula cluster visible in my volume maps that doesn't show up when I project it on the surface.
Is that because dACC/insula is not included in surfaces on Freesurfer?
Thanks!
Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srishtig@email.unc.edu skype: srishti.goel12
It should be included. But dACC and insula are not close to each other. How can there be a cluster that spans both?
On 6/23/18 7:54 PM, srishti goel wrote:
External Email - Use Caution
Hello,
I am using mri_vol2surf to project my volume maps on to the surface. There is a dACC/insula cluster visible in my volume maps that doesn't show up when I project it on the surface.
Is that because dACC/insula is not included in surfaces on Freesurfer?
Thanks!
Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srishtig@email.unc.edu mailto:srishtig@email.unc.edu skype: srishti.goel12
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
They are separate clusters not the same clusters but we both of those don't show up when we project the volume maps on surface. Every other cluster comes up and this has happened in about 2-3 files. Are you absolutely sure that the surface in freesurfer includes dACC and insula?
Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srishtig@email.unc.edu skype: srishti.goel12
On Mon, Jun 25, 2018 at 10:14 AM, Douglas Greve dgreve@mgh.harvard.edu wrote:
It should be included. But dACC and insula are not close to each other. How can there be a cluster that spans both?
On 6/23/18 7:54 PM, srishti goel wrote:
External Email - Use CautionHello,
I am using mri_vol2surf to project my volume maps on to the surface. There is a dACC/insula cluster visible in my volume maps that doesn't show up when I project it on the surface.
Is that because dACC/insula is not included in surfaces on Freesurfer?
Thanks!
Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srishtig@email.unc.edu skype: srishti.goel12
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://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.
Hi Srishti
you should be able to load the volumetric maps with the surfaces and make sure that your clusters are contained within the surface.
cheers Bruce On Mon, 25 Jun 2018, srishti goel wrote:
External Email - Use Caution
They are separate clusters not the same clusters but we both of those don't show up when we project the volume maps on surface. Every other cluster comes up and this has happened in about 2-3 files. Are you absolutely sure that the surface in freesurfer includes dACC and insula?
Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srishtig@email.unc.edu skype: srishti.goel12
On Mon, Jun 25, 2018 at 10:14 AM, Douglas Greve dgreve@mgh.harvard.edu wrote:
It should be included. But dACC and insula are not close to each other. How can there be a cluster that spans both? On 6/23/18 7:54 PM, srishti goel wrote: External Email - Use Caution Hello,I am using mri_vol2surf to project my volume maps on to the surface. There is a dACC/insula cluster visible in my volume maps that doesn't show up when I project it on the surface.
Is that because dACC/insula is not included in surfaces on Freesurfer?
Thanks!
Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srishtig@email.unc.edu skype: srishti.goel12
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.
External Email - Use Caution
Hi Bruce,
Thank you so much for your prompt help. Can I achieve that with:
tkregisterfv --mov [your volume maps] --regheader --s [the subject on whose surface map is registered] --surfs --reg [file name]
Best, Srishti
Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srishtig@email.unc.edu skype: srishti.goel12
On Mon, Jun 25, 2018 at 11:50 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Srishti
you should be able to load the volumetric maps with the surfaces and make sure that your clusters are contained within the surface.
cheers Bruce
On Mon, 25 Jun 2018, srishti goel wrote:
External Email - Use CautionThey are separate clusters not the same clusters but we both of those don't show up when we project the volume maps on surface. Every other cluster comes up and this has happened in about 2-3 files. Are you absolutely sure that the surface in freesurfer includes dACC and insula?
Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srishtig@email.unc.edu skype: srishti.goel12
On Mon, Jun 25, 2018 at 10:14 AM, Douglas Greve dgreve@mgh.harvard.edu wrote:
It should be included. But dACC and insula are not close to eachother. How can there be a cluster that spans both?
On 6/23/18 7:54 PM, srishti goel wrote: External Email - Use Caution Hello,I am using mri_vol2surf to project my volume maps on to the surface. There is a dACC/insula cluster visible in my volume maps that doesn't show up when I project it on the surface.
Is that because dACC/insula is not included in surfaces on Freesurfer?
Thanks!
Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srishtig@email.unc.edu skype: srishti.goel12
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.
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.
External Email - Use Caution
Hello Bruce,
You had mentioned about loading the volumetric maps with the surface to check that all my clusters are contained within the surfaces. Since I am very new to freesurfer, could you please guide to where I can find an appropriate command to do that.
Thank you so much for all the help!
Best, Srishti
Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srishtig@email.unc.edu skype: srishti.goel12
On Mon, Jun 25, 2018 at 11:50 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Srishti
you should be able to load the volumetric maps with the surfaces and make sure that your clusters are contained within the surface.
cheers Bruce
On Mon, 25 Jun 2018, srishti goel wrote:
External Email - Use CautionThey are separate clusters not the same clusters but we both of those don't show up when we project the volume maps on surface. Every other cluster comes up and this has happened in about 2-3 files. Are you absolutely sure that the surface in freesurfer includes dACC and insula?
Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srishtig@email.unc.edu skype: srishti.goel12
On Mon, Jun 25, 2018 at 10:14 AM, Douglas Greve dgreve@mgh.harvard.edu wrote:
It should be included. But dACC and insula are not close to eachother. How can there be a cluster that spans both?
On 6/23/18 7:54 PM, srishti goel wrote: External Email - Use Caution Hello,I am using mri_vol2surf to project my volume maps on to the surface. There is a dACC/insula cluster visible in my volume maps that doesn't show up when I project it on the surface.
Is that because dACC/insula is not included in surfaces on Freesurfer?
Thanks!
Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srishtig@email.unc.edu skype: srishti.goel12
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.
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.
you can try tkmeditfv subject orig.mgz -surfs -ov clustermap.nii.gz -fminmax .01 3 you may have to adjust the thresholds (fminmax)
On 6/26/18 10:43 PM, srishti goel wrote:
External Email - Use Caution
Hello Bruce,
You had mentioned about loading the volumetric maps with the surface to check that all my clusters are contained within the surfaces. Since I am very new to freesurfer, could you please guide to where I can find an appropriate command to do that.
Thank you so much for all the help!
Best, Srishti
Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srishtig@email.unc.edu mailto:srishtig@email.unc.edu skype: srishti.goel12
On Mon, Jun 25, 2018 at 11:50 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> wrote:
Hi Srishti you should be able to load the volumetric maps with the surfaces and make sure that your clusters are contained within the surface. cheers Bruce On Mon, 25 Jun 2018, srishti goel wrote: External Email - Use Caution They are separate clusters not the same clusters but we both of those don't show up when we project the volume maps on surface. Every other cluster comes up and this has happened in about 2-3 files. Are you absolutely sure that the surface in freesurfer includes dACC and insula? Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srishtig@email.unc.edu <mailto:srishtig@email.unc.edu> skype: srishti.goel12 On Mon, Jun 25, 2018 at 10:14 AM, Douglas Greve <dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>> wrote: It should be included. But dACC and insula are not close to each other. How can there be a cluster that spans both? On 6/23/18 7:54 PM, srishti goel wrote: External Email - Use Caution Hello, I am using mri_vol2surf to project my volume maps on to the surface. There is a dACC/insula cluster visible in my volume maps that doesn't show up when I project it on the surface. Is that because dACC/insula is not included in surfaces on Freesurfer? Thanks! Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srishtig@email.unc.edu <mailto:srishtig@email.unc.edu> skype: srishti.goel12 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <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 <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <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
External Email - Use Caution
Hello Bruce,
As suggested by you, I used tkmeditfv to view the volumetric maps on the surface and it seems like the dACC cluster is lying outside the brain. I checked the registration of the volumetric file using tkregisterfv but surprisingly nothing shows up. I also tried using bbregister and then checked the registration but the same thing happened, the volumetric map doesn't show up in either of those cases.
I am confused, as to why that is happening and how can I fix it such that all the clusters are appropriately aligned.
The files I am using have been exported from neuroelf program. I exported them as analyze format (.img and .hdr) and then converted it to nifti format using mri_convert. However, with both the analyze and nifti format, similar things happened.
Any help is highly appreciated.
Thanks, Srishti
Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srishtig@email.unc.edu skype: srishti.goel12
On Tue, Jun 26, 2018 at 11:56 PM, Douglas Greve dgreve@mgh.harvard.edu wrote:
you can try tkmeditfv subject orig.mgz -surfs -ov clustermap.nii.gz -fminmax .01 3 you may have to adjust the thresholds (fminmax)
On 6/26/18 10:43 PM, srishti goel wrote:
External Email - Use CautionHello Bruce,
You had mentioned about loading the volumetric maps with the surface to check that all my clusters are contained within the surfaces. Since I am very new to freesurfer, could you please guide to where I can find an appropriate command to do that.
Thank you so much for all the help!
Best, Srishti
Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srishtig@email.unc.edu skype: srishti.goel12
On Mon, Jun 25, 2018 at 11:50 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu
wrote:
Hi Srishti
you should be able to load the volumetric maps with the surfaces and make sure that your clusters are contained within the surface.
cheers Bruce
On Mon, 25 Jun 2018, srishti goel wrote:
External Email - Use CautionThey are separate clusters not the same clusters but we both of those don't show up when we project the volume maps on surface. Every other cluster comes up and this has happened in about 2-3 files. Are you absolutely sure that the surface in freesurfer includes dACC and insula?
Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srishtig@email.unc.edu skype: srishti.goel12
On Mon, Jun 25, 2018 at 10:14 AM, Douglas Greve dgreve@mgh.harvard.edu wrote:
It should be included. But dACC and insula are not close to eachother. How can there be a cluster that spans both?
On 6/23/18 7:54 PM, srishti goel wrote: External Email - Use Caution Hello,I am using mri_vol2surf to project my volume maps on to the surface. There is a dACC/insula cluster visible in my volume maps that doesn't show up when I project it on the surface.
Is that because dACC/insula is not included in surfaces on Freesurfer?
Thanks!
Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srishtig@email.unc.edu skype: srishti.goel12
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.
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 listFreesurfer@nmr.mgh.harvard.eduhttps://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.
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Douglas Greve -
srishti goel