Hi,
I'm trying to compare analyses that I've done entirely on the surface to analyses I've done in the volume. I'm comparing the analyses by projecting the volume analyses to the surface (HCP's 32k_fs_LR).
The commands I'm using are: mri_vol2surf --mov $niftiFile --mni152reg --hemi ${hemi} --projfrac-max 0 1 0.2 --o ${giftiFile}.$hemi.gii; mri_surf2surf --srcsubject fsaverage --srcsurfval ${giftiFile}.$hemi.gii --trgsubject 32k_fs_LR --trgsurfval ${giftiFile}.$hemi.gii --hemi ${hemi}; It seems that the FSL volumes look identical to the surface analysis, when mapped. (Our surface analysis is mainly FSL-based, so this makes sense.) The SPM mapping, however, looks very odd. It isn't just that the intensity differs, but the localization of high intensity areas also varies. It seems that everything is shifted a bit superior and, possibly, posterior to the true location (as seen on the surface analysis).
I'm wondering if I'm doing anything obviously wrong in my command usage. The brains were normalized to the MNI ICBM 152 template in SPM. I *think* it's suitable to use the -mni152reg flag in the command.
I can attach pictures of the comparison if you'd like.
Thanks in advance, Rita
The --mni152reg flag is only appropriate if the mov file is in the 2mm mni152 space. The inclusion of fsaverage as the source subject indicates some ambiguity about this
On 4/3/17 1:56 PM, Rita Elena Loiotile wrote:
Hi,
I'm trying to compare analyses that I've done entirely on the surface to analyses I've done in the volume. I'm comparing the analyses by projecting the volume analyses to the surface (HCP's 32k_fs_LR).
The commands I'm using are: mri_vol2surf --mov $niftiFile --mni152reg --hemi ${hemi} --projfrac-max 0 1 0.2 --o ${giftiFile}.$hemi.gii; mri_surf2surf --srcsubject fsaverage --srcsurfval ${giftiFile}.$hemi.gii --trgsubject 32k_fs_LR --trgsurfval ${giftiFile}.$hemi.gii --hemi ${hemi};It seems that the FSL volumes look identical to the surface analysis, when mapped. (Our surface analysis is mainly FSL-based, so this makes sense.) The SPM mapping, however, looks very odd. It isn't just that the intensity differs, but the localization of high intensity areas also varies. It seems that everything is shifted a bit superior and, possibly, posterior to the true location (as seen on the surface analysis). I'm wondering if I'm doing anything obviously wrong in my command usage. The brains were normalized to the MNI ICBM 152 template in SPM. I *think* it's suitable to use the -mni152reg flag in the command.
I can attach pictures of the comparison if you'd like.
Thanks in advance, Rita
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug,
Thanks for the email. It is in 3mm space, so I guess I should reslice. Can you please clarify the comment about fsaverage? Does the --mni152reg flag not apply to that subject? I'm not sure what you mean about the inclusion indicating ambiguity.
Thanks again, Rita
On Tue, Apr 4, 2017 at 9:21 PM, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
The --mni152reg flag is only appropriate if the mov file is in the 2mm mni152 space. The inclusion of fsaverage as the source subject indicates some ambiguity about this
On 4/3/17 1:56 PM, Rita Elena Loiotile wrote:
Hi,
I'm trying to compare analyses that I've done entirely on the surface to analyses I've done in the volume. I'm comparing the analyses by projecting the volume analyses to the surface (HCP's 32k_fs_LR).
The commands I'm using are: mri_vol2surf --mov $niftiFile --mni152reg --hemi ${hemi} --projfrac-max 0 1 0.2 --o ${giftiFile}.$hemi.gii; mri_surf2surf --srcsubject fsaverage --srcsurfval ${giftiFile}.$hemi.gii --trgsubject 32k_fs_LR --trgsurfval ${giftiFile}.$hemi.gii --hemi ${hemi}; It seems that the FSL volumes look identical to the surface analysis, when mapped. (Our surface analysis is mainly FSL-based, so this makes sense.) The SPM mapping, however, looks very odd. It isn't just that the intensity differs, but the localization of high intensity areas also varies. It seems that everything is shifted a bit superior and, possibly, posterior to the true location (as seen on the surface analysis). I'm wondering if I'm doing anything obviously wrong in my command usage. The brains were normalized to the MNI ICBM 152 template in SPM. I *think* it's suitable to use the -mni152reg flag in the command.
I can attach pictures of the comparison if you'd like.
Thanks in advance, Rita
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.
If you have a 3mm MNI152 space, then you should run bbregister to fsaverage to create a new register.dat file. Alternatively, you can register it directly to 32k_fs_LR and cut out the middle man (make sure to use --9 to account for scaling). Please ignore my comment about fsaverage. In that case it was actually fine.
On 4/4/17 9:40 PM, Rita Elena Loiotile wrote:
Hi Doug,
Thanks for the email. It is in 3mm space, so I guess I should reslice. Can you please clarify the comment about fsaverage? Does the --mni152reg flag not apply to that subject? I'm not sure what you mean about the inclusion indicating ambiguity.
Thanks again, Rita
On Tue, Apr 4, 2017 at 9:21 PM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
The --mni152reg flag is only appropriate if the mov file is in the 2mm mni152 space. The inclusion of fsaverage as the source subject indicates some ambiguity about this On 4/3/17 1:56 PM, Rita Elena Loiotile wrote:Hi, I'm trying to compare analyses that I've done entirely on the surface to analyses I've done in the volume. I'm comparing the analyses by projecting the volume analyses to the surface (HCP's 32k_fs_LR). The commands I'm using are: mri_vol2surf --mov $niftiFile --mni152reg --hemi ${hemi} --projfrac-max 0 1 0.2 --o ${giftiFile}.$hemi.gii; mri_surf2surf --srcsubject fsaverage --srcsurfval ${giftiFile}.$hemi.gii --trgsubject 32k_fs_LR --trgsurfval ${giftiFile}.$hemi.gii --hemi ${hemi};It seems that the FSL volumes look identical to the surface analysis, when mapped. (Our surface analysis is mainly FSL-based, so this makes sense.) The SPM mapping, however, looks very odd. It isn't just that the intensity differs, but the localization of high intensity areas also varies. It seems that everything is shifted a bit superior and, possibly, posterior to the true location (as seen on the surface analysis). I'm wondering if I'm doing anything obviously wrong in my command usage. The brains were normalized to the MNI ICBM 152 template in SPM. I *think* it's suitable to use the -mni152reg flag in the command. I can attach pictures of the comparison if you'd like. Thanks in advance, Rita _______________________________________________ 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi,
I just noticed that when I open my volume file in tksurfer using --overlay it gives a better volume to surface mapping than when I do mri_vol2surf. Do you know what .dat file is used implicitly when tksurfer is called with a volume overlay? It also seems to work well when the subject is fsaverage and when it is 32k_fs_LR. Thank you.
On Wed, Apr 5, 2017 at 9:54 AM, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
If you have a 3mm MNI152 space, then you should run bbregister to fsaverage to create a new register.dat file. Alternatively, you can register it directly to 32k_fs_LR and cut out the middle man (make sure to use --9 to account for scaling). Please ignore my comment about fsaverage. In that case it was actually fine.
On 4/4/17 9:40 PM, Rita Elena Loiotile wrote:
Hi Doug,
Thanks for the email. It is in 3mm space, so I guess I should reslice. Can you please clarify the comment about fsaverage? Does the --mni152reg flag not apply to that subject? I'm not sure what you mean about the inclusion indicating ambiguity.
Thanks again, Rita
On Tue, Apr 4, 2017 at 9:21 PM, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
The --mni152reg flag is only appropriate if the mov file is in the 2mm mni152 space. The inclusion of fsaverage as the source subject indicates some ambiguity about this
On 4/3/17 1:56 PM, Rita Elena Loiotile wrote:
Hi,
I'm trying to compare analyses that I've done entirely on the surface to analyses I've done in the volume. I'm comparing the analyses by projecting the volume analyses to the surface (HCP's 32k_fs_LR).
The commands I'm using are: mri_vol2surf --mov $niftiFile --mni152reg --hemi ${hemi} --projfrac-max 0 1 0.2 --o ${giftiFile}.$hemi.gii; mri_surf2surf --srcsubject fsaverage --srcsurfval ${giftiFile}.$hemi.gii --trgsubject 32k_fs_LR --trgsurfval ${giftiFile}.$hemi.gii --hemi ${hemi}; It seems that the FSL volumes look identical to the surface analysis, when mapped. (Our surface analysis is mainly FSL-based, so this makes sense.) The SPM mapping, however, looks very odd. It isn't just that the intensity differs, but the localization of high intensity areas also varies. It seems that everything is shifted a bit superior and, possibly, posterior to the true location (as seen on the surface analysis). I'm wondering if I'm doing anything obviously wrong in my command usage. The brains were normalized to the MNI ICBM 152 template in SPM. I *think* it's suitable to use the -mni152reg flag in the command.
I can attach pictures of the comparison if you'd like.
Thanks in advance, Rita
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.e du/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.
should be the same as when you use --regheader with tkregister
On 02/09/2018 11:24 PM, Rita Elena Loiotile wrote:
Hi,
I just noticed that when I open my volume file in tksurfer using --overlay it gives a better volume to surface mapping than when I do mri_vol2surf. Do you know what .dat file is used implicitly when tksurfer is called with a volume overlay? It also seems to work well when the subject is fsaverage and when it is 32k_fs_LR. Thank you.
On Wed, Apr 5, 2017 at 9:54 AM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
If you have a 3mm MNI152 space, then you should run bbregister to fsaverage to create a new register.dat file. Alternatively, you can register it directly to 32k_fs_LR and cut out the middle man (make sure to use --9 to account for scaling). Please ignore my comment about fsaverage. In that case it was actually fine. On 4/4/17 9:40 PM, Rita Elena Loiotile wrote:Hi Doug, Thanks for the email. It is in 3mm space, so I guess I should reslice. Can you please clarify the comment about fsaverage? Does the --mni152reg flag not apply to that subject? I'm not sure what you mean about the inclusion indicating ambiguity. Thanks again, Rita On Tue, Apr 4, 2017 at 9:21 PM, Douglas Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: The --mni152reg flag is only appropriate if the mov file is in the 2mm mni152 space. The inclusion of fsaverage as the source subject indicates some ambiguity about this On 4/3/17 1:56 PM, Rita Elena Loiotile wrote:Hi, I'm trying to compare analyses that I've done entirely on the surface to analyses I've done in the volume. I'm comparing the analyses by projecting the volume analyses to the surface (HCP's 32k_fs_LR). The commands I'm using are: mri_vol2surf --mov $niftiFile --mni152reg --hemi ${hemi} --projfrac-max 0 1 0.2 --o ${giftiFile}.$hemi.gii; mri_surf2surf --srcsubject fsaverage --srcsurfval ${giftiFile}.$hemi.gii --trgsubject 32k_fs_LR --trgsurfval ${giftiFile}.$hemi.gii --hemi ${hemi};It seems that the FSL volumes look identical to the surface analysis, when mapped. (Our surface analysis is mainly FSL-based, so this makes sense.) The SPM mapping, however, looks very odd. It isn't just that the intensity differs, but the localization of high intensity areas also varies. It seems that everything is shifted a bit superior and, possibly, posterior to the true location (as seen on the surface analysis). I'm wondering if I'm doing anything obviously wrong in my command usage. The brains were normalized to the MNI ICBM 152 template in SPM. I *think* it's suitable to use the -mni152reg flag in the command. I can attach pictures of the comparison if you'd like. Thanks in advance, Rita _______________________________________________ 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>_______________________________________________ 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.
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freesurfer@nmr.mgh.harvard.edu
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Douglas Greve -
Douglas N Greve
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Rita Elena Loiotile