Hi all,
I need a volume that maps my sulci. So first I've run recon-all on my data. Worked like a charm. Visual verification in freeview shows that the inflated surface looks just about right (although it does not seem to be registered to the aparc+aseg volume). However, when I try to run mri_surf2vol, I get the error message "ERROR: cannot recognize the type of surf/lh.inflated".
My precise syntax was mri_surf2vol --o out.nii --identity casestudy2 --surf inflated --hemi --lh --surfval surf/lh.inflated
Can anyone advise me on this?
Best regards,
Lukas
PS :I'm running on FS version 5.3.0. PPS: Is it possible to achieve this from freeview rather than from the command line?
Hi all,
here's my follow-up: I've now tried to use mris_fill on my lh.sulc. However, I got the error message that "there are many more faces than vertices". Running recon-all on this dataset takes 30+ hours on my machine, hence I don't want to do it again unless it is absolutely necessary.
Can anybody recommend another way (or a solution to either my mri_surf2vol or mris_fill problems) of obtaining a binary sulcus mask? I'm in desperate need of one..
Best regards,
Lukas
On 12.05.2017 16:18, Lukas Pezenka wrote:
Hi all,
I need a volume that maps my sulci. So first I've run recon-all on my data. Worked like a charm. Visual verification in freeview shows that the inflated surface looks just about right (although it does not seem to be registered to the aparc+aseg volume). However, when I try to run mri_surf2vol, I get the error message "ERROR: cannot recognize the type of surf/lh.inflated".
My precise syntax was mri_surf2vol --o out.nii --identity casestudy2 --surf inflated --hemi --lh --surfval surf/lh.inflated
Can anyone advise me on this?
Best regards,
Lukas
PS :I'm running on FS version 5.3.0. PPS: Is it possible to achieve this from freeview rather than from the command line? _______________________________________________ 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 Lukas
lh.sulc is not a surface - it's a scalar field over the surface. Have you looked at the wmparc? Does it not fill your needs?
cheers Bruce
On Mon, 15 May 2017, Lukas Pezenka wrote:
Hi all,
here's my follow-up: I've now tried to use mris_fill on my lh.sulc. However, I got the error message that "there are many more faces than vertices". Running recon-all on this dataset takes 30+ hours on my machine, hence I don't want to do it again unless it is absolutely necessary.
Can anybody recommend another way (or a solution to either my mri_surf2vol or mris_fill problems) of obtaining a binary sulcus mask? I'm in desperate need of one..
Best regards,
Lukas
On 12.05.2017 16:18, Lukas Pezenka wrote:
Hi all,
I need a volume that maps my sulci. So first I've run recon-all on my data. Worked like a charm. Visual verification in freeview shows that the inflated surface looks just about right (although it does not seem to be registered to the aparc+aseg volume). However, when I try to run mri_surf2vol, I get the error message "ERROR: cannot recognize the type of surf/lh.inflated".
My precise syntax was mri_surf2vol --o out.nii --identity casestudy2 --surf inflated --hemi --lh --surfval surf/lh.inflated
Can anyone advise me on this?
Best regards,
Lukas
PS :I'm running on FS version 5.3.0. PPS: Is it possible to achieve this from freeview rather than from the command line? _______________________________________________ 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
Hi Bruce,
not sure - from what I see, sulci are labelled as 0 in the wmparc, are they not? In my understanding, only gyri are actually labelled... I might as well get that totally wrong, though, so sorry if I do...
Best regards,
Lukas
On 15.05.2017 15:53, Bruce Fischl wrote:
Hi Lukas
lh.sulc is not a surface - it's a scalar field over the surface. Have you looked at the wmparc? Does it not fill your needs?
cheers Bruce
On Mon, 15 May 2017, Lukas Pezenka wrote:
Hi all,
here's my follow-up: I've now tried to use mris_fill on my lh.sulc. However, I got the error message that "there are many more faces than vertices". Running recon-all on this dataset takes 30+ hours on my machine, hence I don't want to do it again unless it is absolutely necessary.
Can anybody recommend another way (or a solution to either my mri_surf2vol or mris_fill problems) of obtaining a binary sulcus mask? I'm in desperate need of one..
Best regards,
Lukas
On 12.05.2017 16:18, Lukas Pezenka wrote:
Hi all,
I need a volume that maps my sulci. So first I've run recon-all on my data. Worked like a charm. Visual verification in freeview shows that the inflated surface looks just about right (although it does not seem to be registered to the aparc+aseg volume). However, when I try to run mri_surf2vol, I get the error message "ERROR: cannot recognize the type of surf/lh.inflated".
My precise syntax was mri_surf2vol --o out.nii --identity casestudy2 --surf inflated --hemi --lh --surfval surf/lh.inflated
Can anyone advise me on this?
Best regards,
Lukas
PS :I'm running on FS version 5.3.0. PPS: Is it possible to achieve this from freeview rather than from the command line? _______________________________________________ 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
no, they shouldn't be labeled as 0. You can create your own though, possibly using Christophe's parcellation instead of the aparc.annot (check in recon-all.cmd to see how to run it). Christophe's has sulci labeled separately so might be better for your purposes. Or you could create your own from your own label(s) On Mon, 15 May 2017, Lukas Pezenka wrote:
Hi Bruce,
not sure - from what I see, sulci are labelled as 0 in the wmparc, are they not? In my understanding, only gyri are actually labelled... I might as well get that totally wrong, though, so sorry if I do...
Best regards,
Lukas
On 15.05.2017 15:53, Bruce Fischl wrote:
Hi Lukas
lh.sulc is not a surface - it's a scalar field over the surface. Have you looked at the wmparc? Does it not fill your needs?
cheers Bruce
On Mon, 15 May 2017, Lukas Pezenka wrote:
Hi all,
here's my follow-up: I've now tried to use mris_fill on my lh.sulc. However, I got the error message that "there are many more faces than vertices". Running recon-all on this dataset takes 30+ hours on my machine, hence I don't want to do it again unless it is absolutely necessary.
Can anybody recommend another way (or a solution to either my mri_surf2vol or mris_fill problems) of obtaining a binary sulcus mask? I'm in desperate need of one..
Best regards,
Lukas
On 12.05.2017 16:18, Lukas Pezenka wrote:
Hi all,
I need a volume that maps my sulci. So first I've run recon-all on my data. Worked like a charm. Visual verification in freeview shows that the inflated surface looks just about right (although it does not seem to be registered to the aparc+aseg volume). However, when I try to run mri_surf2vol, I get the error message "ERROR: cannot recognize the type of surf/lh.inflated".
My precise syntax was mri_surf2vol --o out.nii --identity casestudy2 --surf inflated --hemi --lh --surfval surf/lh.inflated
Can anyone advise me on this?
Best regards,
Lukas
PS :I'm running on FS version 5.3.0. PPS: Is it possible to achieve this from freeview rather than from the command line? _______________________________________________ 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
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
Thank you. The tip about Christophe's parcellation was very helpful - I can actually see the sulcal labels in freesurfer when loading aparc.a2009s+aparc volume. Oddly enough, when I check the "show existing labels only" box, none of them is displayed - I wonder why that is?
I should, in any case, be able to build the map now. Thank you!
Best regards,
Lukas
On 15.05.2017 18:38, Bruce Fischl wrote:
no, they shouldn't be labeled as 0. You can create your own though, possibly using Christophe's parcellation instead of the aparc.annot (check in recon-all.cmd to see how to run it). Christophe's has sulci labeled separately so might be better for your purposes. Or you could create your own from your own label(s) On Mon, 15 May 2017, Lukas Pezenka wrote:
Hi Bruce,
not sure - from what I see, sulci are labelled as 0 in the wmparc, are they not? In my understanding, only gyri are actually labelled... I might as well get that totally wrong, though, so sorry if I do...
Best regards,
Lukas
On 15.05.2017 15:53, Bruce Fischl wrote:
Hi Lukas
lh.sulc is not a surface - it's a scalar field over the surface. Have you looked at the wmparc? Does it not fill your needs?
cheers Bruce
On Mon, 15 May 2017, Lukas Pezenka wrote:
Hi all,
here's my follow-up: I've now tried to use mris_fill on my lh.sulc. However, I got the error message that "there are many more faces than vertices". Running recon-all on this dataset takes 30+ hours on my machine, hence I don't want to do it again unless it is absolutely necessary.
Can anybody recommend another way (or a solution to either my mri_surf2vol or mris_fill problems) of obtaining a binary sulcus mask? I'm in desperate need of one..
Best regards,
Lukas
On 12.05.2017 16:18, Lukas Pezenka wrote:
Hi all,
I need a volume that maps my sulci. So first I've run recon-all on my data. Worked like a charm. Visual verification in freeview shows that the inflated surface looks just about right (although it does not seem to be registered to the aparc+aseg volume). However, when I try to run mri_surf2vol, I get the error message "ERROR: cannot recognize the type of surf/lh.inflated".
My precise syntax was mri_surf2vol --o out.nii --identity casestudy2 --surf inflated --hemi --lh --surfval surf/lh.inflated
Can anyone advise me on this?
Best regards,
Lukas
PS :I'm running on FS version 5.3.0. PPS: Is it possible to achieve this from freeview rather than from the command line? _______________________________________________ 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
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
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hmm, not sure. Ruopeng?
On Mon, 15 May 2017, Lukas Pezenka wrote:
Thank you. The tip about Christophe's parcellation was very helpful - I can actually see the sulcal labels in freesurfer when loading aparc.a2009s+aparc volume. Oddly enough, when I check the "show existing labels only" box, none of them is displayed - I wonder why that is?
I should, in any case, be able to build the map now. Thank you!
Best regards,
Lukas
On 15.05.2017 18:38, Bruce Fischl wrote:
no, they shouldn't be labeled as 0. You can create your own though, possibly using Christophe's parcellation instead of the aparc.annot (check in recon-all.cmd to see how to run it). Christophe's has sulci labeled separately so might be better for your purposes. Or you could create your own from your own label(s) On Mon, 15 May 2017, Lukas Pezenka wrote:
Hi Bruce,
not sure - from what I see, sulci are labelled as 0 in the wmparc, are they not? In my understanding, only gyri are actually labelled... I might as well get that totally wrong, though, so sorry if I do...
Best regards,
Lukas
On 15.05.2017 15:53, Bruce Fischl wrote:
Hi Lukas
lh.sulc is not a surface - it's a scalar field over the surface. Have you looked at the wmparc? Does it not fill your needs?
cheers Bruce
On Mon, 15 May 2017, Lukas Pezenka wrote:
Hi all,
here's my follow-up: I've now tried to use mris_fill on my lh.sulc. However, I got the error message that "there are many more faces than vertices". Running recon-all on this dataset takes 30+ hours on my machine, hence I don't want to do it again unless it is absolutely necessary.
Can anybody recommend another way (or a solution to either my mri_surf2vol or mris_fill problems) of obtaining a binary sulcus mask? I'm in desperate need of one..
Best regards,
Lukas
On 12.05.2017 16:18, Lukas Pezenka wrote:
Hi all,
I need a volume that maps my sulci. So first I've run recon-all on my data. Worked like a charm. Visual verification in freeview shows that the inflated surface looks just about right (although it does not seem to be registered to the aparc+aseg volume). However, when I try to run mri_surf2vol, I get the error message "ERROR: cannot recognize the type of surf/lh.inflated".
My precise syntax was mri_surf2vol --o out.nii --identity casestudy2 --surf inflated --hemi --lh --surfval surf/lh.inflated
Can anyone advise me on this?
Best regards,
Lukas
PS :I'm running on FS version 5.3.0. PPS: Is it possible to achieve this from freeview rather than from the command line? _______________________________________________ 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
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Not sure if I followed. Does the look up table have the labels at all?
On May 15, 2017, at 7:46 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
hmm, not sure. Ruopeng?
On Mon, 15 May 2017, Lukas Pezenka wrote:
Thank you. The tip about Christophe's parcellation was very helpful - I can actually see the sulcal labels in freesurfer when loading aparc.a2009s+aparc volume. Oddly enough, when I check the "show existing labels only" box, none of them is displayed - I wonder why that is?
I should, in any case, be able to build the map now. Thank you!
Best regards,
Lukas
On 15.05.2017 18:38, Bruce Fischl wrote:
no, they shouldn't be labeled as 0. You can create your own though, possibly using Christophe's parcellation instead of the aparc.annot (check in recon-all.cmd to see how to run it). Christophe's has sulci labeled separately so might be better for your purposes. Or you could create your own from your own label(s) On Mon, 15 May 2017, Lukas Pezenka wrote:
Hi Bruce,
not sure - from what I see, sulci are labelled as 0 in the wmparc, are they not? In my understanding, only gyri are actually labelled... I might as well get that totally wrong, though, so sorry if I do...
Best regards,
Lukas
On 15.05.2017 15:53, Bruce Fischl wrote:
Hi Lukas
lh.sulc is not a surface - it's a scalar field over the surface. Have you looked at the wmparc? Does it not fill your needs?
cheers Bruce
On Mon, 15 May 2017, Lukas Pezenka wrote:
Hi all,
here's my follow-up: I've now tried to use mris_fill on my lh.sulc. However, I got the error message that "there are many more faces than vertices". Running recon-all on this dataset takes 30+ hours on my machine, hence I don't want to do it again unless it is absolutely necessary.
Can anybody recommend another way (or a solution to either my mri_surf2vol or mris_fill problems) of obtaining a binary sulcus mask? I'm in desperate need of one..
Best regards,
Lukas
On 12.05.2017 16:18, Lukas Pezenka wrote: > Hi all, > > I need a volume that maps my sulci. So first I've run recon-all on my > data. Worked like a charm. Visual verification in freeview shows that > the inflated surface looks just about right (although it does not seem > to be registered to the aparc+aseg volume). However, when I try to run > mri_surf2vol, I get the error message "ERROR: cannot recognize the type > of surf/lh.inflated". > > My precise syntax was mri_surf2vol --o out.nii --identity casestudy2 > --surf inflated --hemi --lh --surfval surf/lh.inflated > > Can anyone advise me on this? > > Best regards, > > Lukas > > PS :I'm running on FS version 5.3.0. > PPS: Is it possible to achieve this from freeview rather than from the > command line? > _______________________________________________ > 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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You need to use a valid output format like mgh, mgz, nii, etc (eg, surf/lh.inflated.mgh). Also, you should not run vol2surf mapping to the inflated surface as this surface is mostly outside the head. Use the default white surface and then visualize on the inflated only
On 05/12/2017 10:18 AM, Lukas Pezenka wrote:
Hi all,
I need a volume that maps my sulci. So first I've run recon-all on my data. Worked like a charm. Visual verification in freeview shows that the inflated surface looks just about right (although it does not seem to be registered to the aparc+aseg volume). However, when I try to run mri_surf2vol, I get the error message "ERROR: cannot recognize the type of surf/lh.inflated".
My precise syntax was mri_surf2vol --o out.nii --identity casestudy2 --surf inflated --hemi --lh --surfval surf/lh.inflated
Can anyone advise me on this?
Best regards,
Lukas
PS :I'm running on FS version 5.3.0. PPS: Is it possible to achieve this from freeview rather than from the command line? _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Douglas N Greve -
Lukas Pezenka -
Ruopeng Wang