[Freesurfer] Parcellated regions as masks?
Hi FS users, We've T1 and EPI images collected. For my analysis I want to use FS parcellated regions (both cortical/sub-cortical regions) as ROIs (Masks) for my functional images. Would anyone kindly let me know what is the best way to proceed. Cheers, Sabin Khadka___ 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.
Re: [Freesurfer] Parcellated regions as masks?
establish a registration between the functional and anatomical with bbregister, then use mri_label2vol to map the aparc+aseg.mgz into the function space. On 01/21/2015 01:52 PM, sabin khadka wrote: Hi FS users, We've T1 and EPI images collected. For my analysis I want to use FS parcellated regions (both cortical/sub-cortical regions) as ROIs (Masks) for my functional images. Would anyone kindly let me know what is the best way to proceed. Cheers, Sabin Khadka ___ 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 gr...@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.
Re: [Freesurfer] Parcellated regions as masks?
If you run it with --help you'll see several examples. On 01/21/2015 03:21 PM, sabin khadka wrote: Hi Doug- Thanks for the reply. Would you mind elaborating on how exactly to use mri_label2vol to map the aparc+aseg.mgz into the function space ( I could not find the correct syntax that should be used)? Also, what should i do if I want individual masks for each ROI? Cheers, Sabin Khadka *From:* Douglas N Greve gr...@nmr.mgh.harvard.edu *To:* freesurfer@nmr.mgh.harvard.edu *Sent:* Wednesday, January 21, 2015 1:59 PM *Subject:* Re: [Freesurfer] Parcellated regions as masks? establish a registration between the functional and anatomical with bbregister, then use mri_label2vol to map the aparc+aseg.mgz into the function space. On 01/21/2015 01:52 PM, sabin khadka wrote: Hi FS users, We've T1 and EPI images collected. For my analysis I want to use FS parcellated regions (both cortical/sub-cortical regions) as ROIs (Masks) for my functional images. Would anyone kindly let me know what is the best way to proceed. Cheers, Sabin Khadka ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@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 mailto: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 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 gr...@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
Re: [Freesurfer] Parcellated regions as masks?
Hi Doug- Thanks for the reply. Would you mind elaborating on how exactly to use mri_label2vol to map the aparc+aseg.mgz into the function space ( I could not find the correct syntax that should be used)? Also, what should i do if I want individual masks for each ROI? Cheers, Sabin Khadka From: Douglas N Greve gr...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, January 21, 2015 1:59 PM Subject: Re: [Freesurfer] Parcellated regions as masks? establish a registration between the functional and anatomical with bbregister, then use mri_label2vol to map the aparc+aseg.mgz into the function space. On 01/21/2015 01:52 PM, sabin khadka wrote: Hi FS users, We've T1 and EPI images collected. For my analysis I want to use FS parcellated regions (both cortical/sub-cortical regions) as ROIs (Masks) for my functional images. Would anyone kindly let me know what is the best way to proceed. Cheers, Sabin Khadka ___ 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 gr...@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 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.
