[Freesurfer] Creating an ROI mask for Cortical Thickness Analysis
Hello Freesurfer’s I am trying to look at the cortical thickness for a specific ROI on the cortical surface (Primary Auditory Cortex: transverse temporal gyri). I found a specific tutorial (https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness) however the tutorial assumes I already have an ROI mask created. I was wondering if anyone had any tips on creating an ROI for the cortical surface from the parcellation/annotation files. I know you can “hand-draw” ROI’s in tkmedit or freeview but I would prefer something less subjective that doesn’t rely on my untrained eye and unsteady hand! Thanks in advance. Best, Michael S. ___ 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] Creating an ROI mask for Cortical Thickness Analysis
Why not just get it from the ?h.aparc.stats file? On 10/22/2014 03:43 PM, Smith, Michael wrote: > Hello Freesurfer’s > > I am trying to look at the cortical thickness for a specific ROI on > the cortical surface (Primary Auditory Cortex: transverse temporal > gyri). I found a specific tutorial > (https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness) > however the tutorial assumes I already have an ROI mask created. I was > wondering if anyone had any tips on creating an ROI for the cortical > surface from the parcellation/annotation files. I know you can > “hand-draw” ROI’s in tkmedit or freeview but I would prefer something > less subjective that doesn’t rely on my untrained eye and unsteady > hand! Thanks in advance. > > Best, > > Michael S. > > > > ___ > 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] Creating an ROI mask for Cortical Thickness Analysis
I guess I'm not entirely sure how to do that? Are there any tutorials on how to extract an ROI from the aparc.stats file? -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Wednesday, October 22, 2014 4:21 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Creating an ROI mask for Cortical Thickness Analysis Why not just get it from the ?h.aparc.stats file? On 10/22/2014 03:43 PM, Smith, Michael wrote: > Hello Freesurfer's > > I am trying to look at the cortical thickness for a specific ROI on > the cortical surface (Primary Auditory Cortex: transverse temporal > gyri). I found a specific tutorial > (https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness) > however the tutorial assumes I already have an ROI mask created. I was > wondering if anyone had any tips on creating an ROI for the cortical > surface from the parcellation/annotation files. I know you can > "hand-draw" ROI's in tkmedit or freeview but I would prefer something > less subjective that doesn't rely on my untrained eye and unsteady > hand! Thanks in advance. > > Best, > > Michael S. > > > > ___ > 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
Re: [Freesurfer] Creating an ROI mask for Cortical Thickness Analysis
Hi Michael you can use mri_annotation2label to extract a specific label from the aparc file and go from there. cheers Bruce On Thu, 23 Oct 2014, Smith, Michael wrote: > I guess I'm not entirely sure how to do that? Are there any tutorials on how > to extract an ROI from the aparc.stats file? > > -Original Message- > From: freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve > Sent: Wednesday, October 22, 2014 4:21 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Creating an ROI mask for Cortical Thickness Analysis > > > Why not just get it from the ?h.aparc.stats file? > > On 10/22/2014 03:43 PM, Smith, Michael wrote: >> Hello Freesurfer's >> >> I am trying to look at the cortical thickness for a specific ROI on >> the cortical surface (Primary Auditory Cortex: transverse temporal >> gyri). I found a specific tutorial >> (https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness) >> however the tutorial assumes I already have an ROI mask created. I was >> wondering if anyone had any tips on creating an ROI for the cortical >> surface from the parcellation/annotation files. I know you can >> "hand-draw" ROI's in tkmedit or freeview but I would prefer something >> less subjective that doesn't rely on my untrained eye and unsteady >> hand! Thanks in advance. >> >> Best, >> >> Michael S. >> >> >> >> ___ >> 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 > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Creating an ROI mask for Cortical Thickness Analysis
It is just a text file, so you can just look in it. You can also run aparcstats2table to extract all ROIs or a particular ROI for a group of subjects. doug On 10/23/2014 09:00 AM, Smith, Michael wrote: > I guess I'm not entirely sure how to do that? Are there any tutorials on how > to extract an ROI from the aparc.stats file? > > -Original Message- > From: freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve > Sent: Wednesday, October 22, 2014 4:21 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Creating an ROI mask for Cortical Thickness Analysis > > > Why not just get it from the ?h.aparc.stats file? > > On 10/22/2014 03:43 PM, Smith, Michael wrote: >> Hello Freesurfer's >> >> I am trying to look at the cortical thickness for a specific ROI on >> the cortical surface (Primary Auditory Cortex: transverse temporal >> gyri). I found a specific tutorial >> (https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness) >> however the tutorial assumes I already have an ROI mask created. I was >> wondering if anyone had any tips on creating an ROI for the cortical >> surface from the parcellation/annotation files. I know you can >> "hand-draw" ROI's in tkmedit or freeview but I would prefer something >> less subjective that doesn't rely on my untrained eye and unsteady >> hand! Thanks in advance. >> >> Best, >> >> Michael S. >> >> >> >> ___ >> 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 > > -- 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] Creating an ROI mask for Cortical Thickness Analysis
Hey Bruce, Never responded but this worked out great thanks for the help. -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Thursday, October 23, 2014 9:31 AM To: Freesurfer support list Subject: Re: [Freesurfer] Creating an ROI mask for Cortical Thickness Analysis Hi Michael you can use mri_annotation2label to extract a specific label from the aparc file and go from there. cheers Bruce On Thu, 23 Oct 2014, Smith, Michael wrote: > I guess I'm not entirely sure how to do that? Are there any tutorials on how > to extract an ROI from the aparc.stats file? > > -Original Message- > From: freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N > Greve > Sent: Wednesday, October 22, 2014 4:21 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Creating an ROI mask for Cortical Thickness > Analysis > > > Why not just get it from the ?h.aparc.stats file? > > On 10/22/2014 03:43 PM, Smith, Michael wrote: >> Hello Freesurfer's >> >> I am trying to look at the cortical thickness for a specific ROI on >> the cortical surface (Primary Auditory Cortex: transverse temporal >> gyri). I found a specific tutorial >> (https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness >> ) however the tutorial assumes I already have an ROI mask created. I >> was wondering if anyone had any tips on creating an ROI for the >> cortical surface from the parcellation/annotation files. I know you >> can "hand-draw" ROI's in tkmedit or freeview but I would prefer >> something less subjective that doesn't rely on my untrained eye and >> unsteady hand! Thanks in advance. >> >> Best, >> >> Michael S. >> >> >> >> ___ >> 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 > > > ___ 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
Re: [Freesurfer] Creating an ROI mask for Cortical Thickness Analysis
glad to hear it Bruce On Tue, 28 Oct 2014, Smith, Michael wrote: > Hey Bruce, > > Never responded but this worked out great thanks for the help. > > -Original Message- > From: freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl > Sent: Thursday, October 23, 2014 9:31 AM > To: Freesurfer support list > Subject: Re: [Freesurfer] Creating an ROI mask for Cortical Thickness Analysis > > Hi Michael > > you can use mri_annotation2label to extract a specific label from the aparc > file and go from there. > > cheers > Bruce > On Thu, 23 Oct 2014, Smith, Michael wrote: > >> I guess I'm not entirely sure how to do that? Are there any tutorials on how >> to extract an ROI from the aparc.stats file? >> >> -Original Message- >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N >> Greve >> Sent: Wednesday, October 22, 2014 4:21 PM >> To: freesurfer@nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] Creating an ROI mask for Cortical Thickness >> Analysis >> >> >> Why not just get it from the ?h.aparc.stats file? >> >> On 10/22/2014 03:43 PM, Smith, Michael wrote: >>> Hello Freesurfer's >>> >>> I am trying to look at the cortical thickness for a specific ROI on >>> the cortical surface (Primary Auditory Cortex: transverse temporal >>> gyri). I found a specific tutorial >>> (https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness >>> ) however the tutorial assumes I already have an ROI mask created. I >>> was wondering if anyone had any tips on creating an ROI for the >>> cortical surface from the parcellation/annotation files. I know you >>> can "hand-draw" ROI's in tkmedit or freeview but I would prefer >>> something less subjective that doesn't rely on my untrained eye and >>> unsteady hand! Thanks in advance. >>> >>> Best, >>> >>> Michael S. >>> >>> >>> >>> ___ >>> 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 >> >> >> > ___ > 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
