Hi, I am using freesurfer for non_human primate. I did the segmentation in freesurfer , at the end i have the wm.mgz but not grey matter since the command to get it during segmentation doesn't work in monkey brain. in the forlder /surf/ i have all files such as lh/rh.pial, curv, sulc, white. Since I am also using SPM and some toolbox to conduct my connectivity data i need good segmentation, so i wanted to use the files in surf, the pial and white to get the grey matter information and then convert it to a volume file. I've been looking for solutions, but didn't find anything, can you help? how shall i proceed to get my grey matter mask from my segmentation, in the native space.
Thank you,
Best regards, Sherihane KUL
you can try mris_volmask or mri_surf2vol. volmask is the better choice if it works for your data. Look in recon-all to see how to call it. This is what creates the ribbon.mgz file, which sounds like what you need
On 11/20/2015 12:28 PM, Sherihane Bensemmane wrote:
Hi, I am using freesurfer for non_human primate. I did the segmentation in freesurfer , at the end i have the wm.mgz but not grey matter since the command to get it during segmentation doesn't work in monkey brain. in the forlder /surf/ i have all files such as lh/rh.pial, curv, sulc, white. Since I am also using SPM and some toolbox to conduct my connectivity data i need good segmentation, so i wanted to use the files in surf, the pial and white to get the grey matter information and then convert it to a volume file. I've been looking for solutions, but didn't find anything, can you help? how shall i proceed to get my grey matter mask from my segmentation, in the native space.
Thank you,
Best regards, Sherihane KUL
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
if i use mri_surf2vol on the pial alone, i would have the entire gray matter?
Best regards, Sherihane Bensemmane PhD Student, Research Group Neurophysiology, K.U. Leuven, O&N II Herestraat 49 - box 1021 3000 Leuven, Belgium
________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Friday, November 20, 2015 6:49 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] exctracting grey matter
you can try mris_volmask or mri_surf2vol. volmask is the better choice if it works for your data. Look in recon-all to see how to call it. This is what creates the ribbon.mgz file, which sounds like what you need
On 11/20/2015 12:28 PM, Sherihane Bensemmane wrote:
Hi, I am using freesurfer for non_human primate. I did the segmentation in freesurfer , at the end i have the wm.mgz but not grey matter since the command to get it during segmentation doesn't work in monkey brain. in the forlder /surf/ i have all files such as lh/rh.pial, curv, sulc, white. Since I am also using SPM and some toolbox to conduct my connectivity data i need good segmentation, so i wanted to use the files in surf, the pial and white to get the grey matter information and then convert it to a volume file. I've been looking for solutions, but didn't find anything, can you help? how shall i proceed to get my grey matter mask from my segmentation, in the native space.
Thank you,
Best regards, Sherihane KUL
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.
no. use --mkmask
On 11/20/2015 12:51 PM, Sherihane Bensemmane wrote:
if i use mri_surf2vol on the pial alone, i would have the entire gray matter?
Best regards, Sherihane Bensemmane PhD Student, Research Group Neurophysiology, K.U. Leuven, O&N II Herestraat 49 - box 1021 3000 Leuven, Belgium
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Friday, November 20, 2015 6:49 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] exctracting grey matter
you can try mris_volmask or mri_surf2vol. volmask is the better choice if it works for your data. Look in recon-all to see how to call it. This is what creates the ribbon.mgz file, which sounds like what you need
On 11/20/2015 12:28 PM, Sherihane Bensemmane wrote:
Hi, I am using freesurfer for non_human primate. I did the segmentation in freesurfer , at the end i have the wm.mgz but not grey matter since the command to get it during segmentation doesn't work in monkey brain. in the forlder /surf/ i have all files such as lh/rh.pial, curv, sulc, white. Since I am also using SPM and some toolbox to conduct my connectivity data i need good segmentation, so i wanted to use the files in surf, the pial and white to get the grey matter information and then convert it to a volume file. I've been looking for solutions, but didn't find anything, can you help? how shall i proceed to get my grey matter mask from my segmentation, in the native space.
Thank you,
Best regards, Sherihane KUL
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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
mris_volmask can't work with my data ( error: mghRead(/data/fmri_monkey_raw/fs/subjects//thelma_anat5/mri/aseg.mgz, -1): could not open file), we can't with the anatomical images we have proceed to the regular segmentation, we skip automatic segmentation because it wouldn't work for monkeys. So, i suspected i must use mri_surf2vol, my problem was that i don t understand which file i should use, how i put the command even using mkmask, i don't understand which inputs, what the command need to have what i really want. Sorry, but i'm a bit confused i'm used to use mri_vol2surf or mri_label2surf, but here, i m not able to find exactly what the command need to work Best regards, Sherihane Bensemmane PhD Student, Research Group Neurophysiology, K.U. Leuven, O&N II Herestraat 49 - box 1021 3000 Leuven, Belgium
________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Friday, November 20, 2015 6:53 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] exctracting grey matter
no. use --mkmask
On 11/20/2015 12:51 PM, Sherihane Bensemmane wrote:
if i use mri_surf2vol on the pial alone, i would have the entire gray matter?
Best regards, Sherihane Bensemmane PhD Student, Research Group Neurophysiology, K.U. Leuven, O&N II Herestraat 49 - box 1021 3000 Leuven, Belgium
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Friday, November 20, 2015 6:49 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] exctracting grey matter
you can try mris_volmask or mri_surf2vol. volmask is the better choice if it works for your data. Look in recon-all to see how to call it. This is what creates the ribbon.mgz file, which sounds like what you need
On 11/20/2015 12:28 PM, Sherihane Bensemmane wrote:
Hi, I am using freesurfer for non_human primate. I did the segmentation in freesurfer , at the end i have the wm.mgz but not grey matter since the command to get it during segmentation doesn't work in monkey brain. in the forlder /surf/ i have all files such as lh/rh.pial, curv, sulc, white. Since I am also using SPM and some toolbox to conduct my connectivity data i need good segmentation, so i wanted to use the files in surf, the pial and white to get the grey matter information and then convert it to a volume file. I've been looking for solutions, but didn't find anything, can you help? how shall i proceed to get my grey matter mask from my segmentation, in the native space.
Thank you,
Best regards, Sherihane KUL
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.
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
did you look at the help?
On 11/20/2015 01:21 PM, Sherihane Bensemmane wrote:
mris_volmask can't work with my data ( error: mghRead(/data/fmri_monkey_raw/fs/subjects//thelma_anat5/mri/aseg.mgz, -1): could not open file), we can't with the anatomical images we have proceed to the regular segmentation, we skip automatic segmentation because it wouldn't work for monkeys. So, i suspected i must use mri_surf2vol, my problem was that i don t understand which file i should use, how i put the command even using mkmask, i don't understand which inputs, what the command need to have what i really want. Sorry, but i'm a bit confused i'm used to use mri_vol2surf or mri_label2surf, but here, i m not able to find exactly what the command need to work Best regards, Sherihane Bensemmane PhD Student, Research Group Neurophysiology, K.U. Leuven, O&N II Herestraat 49 - box 1021 3000 Leuven, Belgium
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Friday, November 20, 2015 6:53 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] exctracting grey matter
no. use --mkmask
On 11/20/2015 12:51 PM, Sherihane Bensemmane wrote:
if i use mri_surf2vol on the pial alone, i would have the entire gray matter?
Best regards, Sherihane Bensemmane PhD Student, Research Group Neurophysiology, K.U. Leuven, O&N II Herestraat 49 - box 1021 3000 Leuven, Belgium
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Friday, November 20, 2015 6:49 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] exctracting grey matter
you can try mris_volmask or mri_surf2vol. volmask is the better choice if it works for your data. Look in recon-all to see how to call it. This is what creates the ribbon.mgz file, which sounds like what you need
On 11/20/2015 12:28 PM, Sherihane Bensemmane wrote:
Hi, I am using freesurfer for non_human primate. I did the segmentation in freesurfer , at the end i have the wm.mgz but not grey matter since the command to get it during segmentation doesn't work in monkey brain. in the forlder /surf/ i have all files such as lh/rh.pial, curv, sulc, white. Since I am also using SPM and some toolbox to conduct my connectivity data i need good segmentation, so i wanted to use the files in surf, the pial and white to get the grey matter information and then convert it to a volume file. I've been looking for solutions, but didn't find anything, can you help? how shall i proceed to get my grey matter mask from my segmentation, in the native space.
Thank you,
Best regards, Sherihane KUL
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.
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Sherihane Bensemmane