Dear Freesurfers,
Is there a way to mask a custom ROI (or label) with a volume / label from automated parcellations?
I have an overlay with fMRI activations and am only interested in the precentral cortex (as segmented in rh.aparc).
I could do masking either on the label level (fMRI activation label * rh.precentral.label) OR on a volume level (fMRI ROI volume * rh.precentral volume)
ultimately, I would only be interested in surface thickness of my fMRI hotspots limited to the precentral cortex.
So the most elegant way would be if there were a function in mri_segstats that allows outputs of thickness values to be "sorted" by the automated parcellation.
But any help leading there is appreciated!
Best, Bastian
Try using mri_binarize on the aparc+aseg.mgz volume (aparc+aseg has the same ROIs as aparc but in volume format). You can map this into your functional space. doug
On 07/25/2014 06:29 AM, Bastian Cheng wrote:
Dear Freesurfers,
Is there a way to mask a custom ROI (or label) with a volume / label from automated parcellations?
I have an overlay with fMRI activations and am only interested in the precentral cortex (as segmented in rh.aparc).
I could do masking either on the label level (fMRI activation label * rh.precentral.label) OR on a volume level (fMRI ROI volume * rh.precentral volume)
ultimately, I would only be interested in surface thickness of my fMRI hotspots limited to the precentral cortex.
So the most elegant way would be if there were a function in mri_segstats that allows outputs of thickness values to be "sorted" by the automated parcellation.
But any help leading there is appreciated!
Best, Bastian _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thank you, Douglas!
Is there a way to mask my functional ROI with these binarized aparc ROIs?
I guess what I want to do is: ROIfunctional * ROI_precentral_binarized > masked ROIfunctional limted to precentral region
best regards, Bastian.
On 28 July 2014 18:25, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
Try using mri_binarize on the aparc+aseg.mgz volume (aparc+aseg has the same ROIs as aparc but in volume format). You can map this into your functional space. doug
On 07/25/2014 06:29 AM, Bastian Cheng wrote:
Dear Freesurfers,
Is there a way to mask a custom ROI (or label) with a volume / label from automated parcellations?
I have an overlay with fMRI activations and am only interested in the precentral cortex (as segmented in rh.aparc).
I could do masking either on the label level (fMRI activation label * rh.precentral.label) OR on a volume level (fMRI ROI volume * rh.precentral volume)
ultimately, I would only be interested in surface thickness of my fMRI hotspots limited to the precentral cortex.
So the most elegant way would be if there were a function in mri_segstats that allows outputs of thickness values to be "sorted" by the automated parcellation.
But any help leading there is appreciated!
Best, Bastian _______________________________________________ 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.
Does mri_mask work?
On 07/28/2014 12:50 PM, Bastian Cheng wrote:
Thank you, Douglas!
Is there a way to mask my functional ROI with these binarized aparc ROIs?
I guess what I want to do is: ROIfunctional * ROI_precentral_binarized > masked ROIfunctional limted to precentral region
best regards, Bastian.
On 28 July 2014 18:25, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
Try using mri_binarize on the aparc+aseg.mgz volume (aparc+aseg has the same ROIs as aparc but in volume format). You can map this into your functional space. doug
On 07/25/2014 06:29 AM, Bastian Cheng wrote:
Dear Freesurfers,
Is there a way to mask a custom ROI (or label) with a volume / label from automated parcellations?
I have an overlay with fMRI activations and am only interested in the precentral cortex (as segmented in rh.aparc).
I could do masking either on the label level (fMRI activation label * rh.precentral.label) OR on a volume level (fMRI ROI volume * rh.precentral volume)
ultimately, I would only be interested in surface thickness of my fMRI hotspots limited to the precentral cortex.
So the most elegant way would be if there were a function in mri_segstats that allows outputs of thickness values to be "sorted" by the automated parcellation.
But any help leading there is appreciated!
Best, Bastian _______________________________________________ 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
works perfectly, thank you!
On 28 July 2014 19:27, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
Does mri_mask work?
On 07/28/2014 12:50 PM, Bastian Cheng wrote:
Thank you, Douglas!
Is there a way to mask my functional ROI with these binarized aparc ROIs?
I guess what I want to do is: ROIfunctional * ROI_precentral_binarized > masked ROIfunctional limted to precentral region
best regards, Bastian.
On 28 July 2014 18:25, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
Try using mri_binarize on the aparc+aseg.mgz volume (aparc+aseg has the same ROIs as aparc but in volume format). You can map this into your functional space. doug
On 07/25/2014 06:29 AM, Bastian Cheng wrote:
Dear Freesurfers,
Is there a way to mask a custom ROI (or label) with a volume / label from automated parcellations?
I have an overlay with fMRI activations and am only interested in the precentral cortex (as segmented in rh.aparc).
I could do masking either on the label level (fMRI activation label * rh.precentral.label) OR on a volume level (fMRI ROI volume * rh.precentral volume)
ultimately, I would only be interested in surface thickness of my fMRI hotspots limited to the precentral cortex.
So the most elegant way would be if there were a function in mri_segstats that allows outputs of thickness values to be "sorted" by the automated parcellation.
But any help leading there is appreciated!
Best, Bastian _______________________________________________ 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@nmr.mgh.harvard.edu
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Bastian Cheng -
Douglas N Greve