Re: [Freesurfer] cortical surface area calculation
Yes, it will On 8/7/2020 6:27 PM, Alexopoulos, Dimitrios wrote: External Email - Use Caution Hi all, Does this command calculate the Cortical Surface Area without the non-cortical Medial Wall?? mris_calc --label ../label/lh.cortex.label lh.area stats Jim The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return 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] cortical surface area
Thank you for the input. Jim -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas Greve Sent: Friday, October 13, 2017 10:09 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] cortical surface area The 2nd is the one you want as the first one includes non cortical structures in the medial wall. On 10/12/17 6:35 PM, Alexopoulos, Dimitrios wrote: > Thanks. > > I ran this command: > mris_anatomical_stats subjectID lh pial > It gave me a total surface area of 115007 mm^2 > > I also tried the following command from within the 'label' directory: > mris_anatomical_stats -l lh.cortex.label -f lh.cortex.stats -b subjectID lh > pial > It gave me a total surface area 109458 mm^2 > > Which is the correct method and value for total cortical surface area? > > Jim > > > -Original Message- > From: freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl > Sent: Thursday, October 12, 2017 5:17 PM > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] cortical surface area > > oh, sorry, I missed the 5.3 part. YOu can always compute it for a subject > via: > > mris_anatomical_stats pial > > cheers > Bruce > On Thu, 12 Oct 2017, > Alexopoulos, Dimitrios wrote: > >> I don't see this file in the stats directory using FS 5.3. >> >> Jim >> >> -Original Message- >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce >> Fischl >> Sent: Thursday, October 12, 2017 4:52 PM >> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> >> Subject: Re: [Freesurfer] cortical surface area >> >> Hi Jim >> >> check the ?h.aparc.pial.stats file. I think the total surface area should be >> in there. >> >> cheers >> Bruce >> On Thu, 12 Oct 2017, Alexopoulos, Dimitrios wrote: >> >>> Specifically, where in the aparc.stats file (or other file) is the cortical >>> surface area? >>> I only see default output for 'WhiteSurfArea'. >>> >>> Jim >>> >>> >>> -Original Message- >>> From: freesurfer-boun...@nmr.mgh.harvard.edu >>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas >>> N Greve >>> Sent: Thursday, October 12, 2017 4:16 PM >>> To: freesurfer@nmr.mgh.harvard.edu >>> Subject: Re: [Freesurfer] cortical surface area >>> >>> mm2 >>> >>> >>> On 10/12/2017 02:15 PM, Alexopoulos, Dimitrios wrote: >>>> What measure is for the cortical surface area? >>>> >>>> The measure in the aparc.stats file states 'WhiteSurfArea' >>>> >>>> Jim >>>> >>>> >>>> - >>>> - >>>> -- >>>> >>>> The materials in this message are private and may contain Protected >>>> Healthcare Information or other information of a sensitive nature. >>>> If you are not the intended recipient, be advised that any >>>> unauthorized use, disclosure, copying or the taking of any action in >>>> reliance on the contents of this information is strictly prohibited. >>>> If you have received this email in error, please immediately notify >>>> the sender via telephone or return 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 >>> >>> >>> The information in this e-mail is intended only for the person to whom
Re: [Freesurfer] cortical surface area
that is the area of the white matter surface in mm2 On 10/12/17 2:15 PM, Alexopoulos, Dimitrios wrote: What measure is for the cortical surface area? The measure in the aparc.stats file states ‘WhiteSurfArea’ Jim The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return 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 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] cortical surface area
The 2nd is the one you want as the first one includes non cortical structures in the medial wall. On 10/12/17 6:35 PM, Alexopoulos, Dimitrios wrote: > Thanks. > > I ran this command: > mris_anatomical_stats subjectID lh pial > It gave me a total surface area of 115007 mm^2 > > I also tried the following command from within the 'label' directory: > mris_anatomical_stats -l lh.cortex.label -f lh.cortex.stats -b subjectID lh > pial > It gave me a total surface area 109458 mm^2 > > Which is the correct method and value for total cortical surface area? > > Jim > > > -Original Message- > From: freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl > Sent: Thursday, October 12, 2017 5:17 PM > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] cortical surface area > > oh, sorry, I missed the 5.3 part. YOu can always compute it for a subject > via: > > mris_anatomical_stats pial > > cheers > Bruce > On Thu, 12 Oct 2017, > Alexopoulos, Dimitrios wrote: > >> I don't see this file in the stats directory using FS 5.3. >> >> Jim >> >> -Original Message- >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce >> Fischl >> Sent: Thursday, October 12, 2017 4:52 PM >> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> >> Subject: Re: [Freesurfer] cortical surface area >> >> Hi Jim >> >> check the ?h.aparc.pial.stats file. I think the total surface area should be >> in there. >> >> cheers >> Bruce >> On Thu, 12 Oct 2017, Alexopoulos, Dimitrios wrote: >> >>> Specifically, where in the aparc.stats file (or other file) is the cortical >>> surface area? >>> I only see default output for 'WhiteSurfArea'. >>> >>> Jim >>> >>> >>> -Original Message- >>> From: freesurfer-boun...@nmr.mgh.harvard.edu >>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas >>> N Greve >>> Sent: Thursday, October 12, 2017 4:16 PM >>> To: freesurfer@nmr.mgh.harvard.edu >>> Subject: Re: [Freesurfer] cortical surface area >>> >>> mm2 >>> >>> >>> On 10/12/2017 02:15 PM, Alexopoulos, Dimitrios wrote: >>>> What measure is for the cortical surface area? >>>> >>>> The measure in the aparc.stats file states 'WhiteSurfArea' >>>> >>>> Jim >>>> >>>> >>>> - >>>> - >>>> -- >>>> >>>> The materials in this message are private and may contain Protected >>>> Healthcare Information or other information of a sensitive nature. >>>> If you are not the intended recipient, be advised that any >>>> unauthorized use, disclosure, copying or the taking of any action in >>>> reliance on the contents of this information is strictly prohibited. >>>> If you have received this email in error, please immediately notify >>>> the sender via telephone or return 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 >>> >>> >>> 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 con
Re: [Freesurfer] cortical surface area
Thanks. I ran this command: mris_anatomical_stats subjectID lh pial It gave me a total surface area of 115007 mm^2 I also tried the following command from within the 'label' directory: mris_anatomical_stats -l lh.cortex.label -f lh.cortex.stats -b subjectID lh pial It gave me a total surface area 109458 mm^2 Which is the correct method and value for total cortical surface area? Jim -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Thursday, October 12, 2017 5:17 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] cortical surface area oh, sorry, I missed the 5.3 part. YOu can always compute it for a subject via: mris_anatomical_stats pial cheers Bruce On Thu, 12 Oct 2017, Alexopoulos, Dimitrios wrote: > I don't see this file in the stats directory using FS 5.3. > > Jim > > -Original Message- > From: freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce > Fischl > Sent: Thursday, October 12, 2017 4:52 PM > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] cortical surface area > > Hi Jim > > check the ?h.aparc.pial.stats file. I think the total surface area should be > in there. > > cheers > Bruce > On Thu, 12 Oct 2017, Alexopoulos, Dimitrios wrote: > >> Specifically, where in the aparc.stats file (or other file) is the cortical >> surface area? >> I only see default output for 'WhiteSurfArea'. >> >> Jim >> >> >> -Original Message- >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas >> N Greve >> Sent: Thursday, October 12, 2017 4:16 PM >> To: freesurfer@nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] cortical surface area >> >> mm2 >> >> >> On 10/12/2017 02:15 PM, Alexopoulos, Dimitrios wrote: >>> >>> What measure is for the cortical surface area? >>> >>> The measure in the aparc.stats file states 'WhiteSurfArea' >>> >>> Jim >>> >>> >>> - >>> - >>> -- >>> >>> The materials in this message are private and may contain Protected >>> Healthcare Information or other information of a sensitive nature. >>> If you are not the intended recipient, be advised that any >>> unauthorized use, disclosure, copying or the taking of any action in >>> reliance on the contents of this information is strictly prohibited. >>> If you have received this email in error, please immediately notify >>> the sender via telephone or return 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 >> >> >> 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. >> >> >> >> The materials in this message are private and may contain Protected >> Healthcare Information or other information of a sensitive nature. If you >> are not the intended recipient, be advised that any unauthorized use, >> disclosure, copying or the taking of any action in reliance on the contents >> of this information is strictly prohibited. If you have received this email >> in error, please immediately notify the sender via telephone or return
Re: [Freesurfer] cortical surface area
oh, sorry, I missed the 5.3 part. YOu can always compute it for a subject via: mris_anatomical_stats pial cheers Bruce On Thu, 12 Oct 2017, Alexopoulos, Dimitrios wrote: > I don't see this file in the stats directory using FS 5.3. > > Jim > > -Original Message- > From: freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl > Sent: Thursday, October 12, 2017 4:52 PM > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] cortical surface area > > Hi Jim > > check the ?h.aparc.pial.stats file. I think the total surface area should be > in there. > > cheers > Bruce > On Thu, 12 Oct 2017, Alexopoulos, Dimitrios wrote: > >> Specifically, where in the aparc.stats file (or other file) is the cortical >> surface area? >> I only see default output for 'WhiteSurfArea'. >> >> Jim >> >> >> -Original Message- >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N >> Greve >> Sent: Thursday, October 12, 2017 4:16 PM >> To: freesurfer@nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] cortical surface area >> >> mm2 >> >> >> On 10/12/2017 02:15 PM, Alexopoulos, Dimitrios wrote: >>> >>> What measure is for the cortical surface area? >>> >>> The measure in the aparc.stats file states 'WhiteSurfArea' >>> >>> Jim >>> >>> - >>> - >>> -- >>> >>> The materials in this message are private and may contain Protected >>> Healthcare Information or other information of a sensitive nature. If >>> you are not the intended recipient, be advised that any unauthorized >>> use, disclosure, copying or the taking of any action in reliance on >>> the contents of this information is strictly prohibited. If you have >>> received this email in error, please immediately notify the sender >>> via telephone or return 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 >> >> >> 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. >> >> >> >> The materials in this message are private and may contain Protected >> Healthcare Information or other information of a sensitive nature. If you >> are not the intended recipient, be advised that any unauthorized use, >> disclosure, copying or the taking of any action in reliance on the contents >> of this information is strictly prohibited. If you have received this email >> in error, please immediately notify the sender via telephone or return 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 > > > The materials in this message are private and may contain Protected > Healthcare Information or other information of a sensitive nature. If you are > not the intended recipient, be advised that any unauthorized use, disclosure, > copying or the taking of any action in reliance on the contents of this > information is strictly prohibited. If you have received this email in error, > please immediately notify the sender via telephone or return 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] cortical surface area
I don't see this file in the stats directory using FS 5.3. Jim -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Thursday, October 12, 2017 4:52 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] cortical surface area Hi Jim check the ?h.aparc.pial.stats file. I think the total surface area should be in there. cheers Bruce On Thu, 12 Oct 2017, Alexopoulos, Dimitrios wrote: > Specifically, where in the aparc.stats file (or other file) is the cortical > surface area? > I only see default output for 'WhiteSurfArea'. > > Jim > > > -Original Message- > From: freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N > Greve > Sent: Thursday, October 12, 2017 4:16 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] cortical surface area > > mm2 > > > On 10/12/2017 02:15 PM, Alexopoulos, Dimitrios wrote: >> >> What measure is for the cortical surface area? >> >> The measure in the aparc.stats file states 'WhiteSurfArea' >> >> Jim >> >> - >> - >> -- >> >> The materials in this message are private and may contain Protected >> Healthcare Information or other information of a sensitive nature. If >> you are not the intended recipient, be advised that any unauthorized >> use, disclosure, copying or the taking of any action in reliance on >> the contents of this information is strictly prohibited. If you have >> received this email in error, please immediately notify the sender >> via telephone or return 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 > > > 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. > > > > The materials in this message are private and may contain Protected > Healthcare Information or other information of a sensitive nature. If you are > not the intended recipient, be advised that any unauthorized use, disclosure, > copying or the taking of any action in reliance on the contents of this > information is strictly prohibited. If you have received this email in error, > please immediately notify the sender via telephone or return 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 The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] cortical surface area
Hi Jim check the ?h.aparc.pial.stats file. I think the total surface area should be in there. cheers Bruce On Thu, 12 Oct 2017, Alexopoulos, Dimitrios wrote: > Specifically, where in the aparc.stats file (or other file) is the cortical > surface area? > I only see default output for 'WhiteSurfArea'. > > Jim > > > -Original Message- > From: freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve > Sent: Thursday, October 12, 2017 4:16 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] cortical surface area > > mm2 > > > On 10/12/2017 02:15 PM, Alexopoulos, Dimitrios wrote: >> >> What measure is for the cortical surface area? >> >> The measure in the aparc.stats file states 'WhiteSurfArea' >> >> Jim >> >> -- >> -- >> >> The materials in this message are private and may contain Protected >> Healthcare Information or other information of a sensitive nature. If >> you are not the intended recipient, be advised that any unauthorized >> use, disclosure, copying or the taking of any action in reliance on >> the contents of this information is strictly prohibited. If you have >> received this email in error, please immediately notify the sender via >> telephone or return 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 > > > 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. > > > > The materials in this message are private and may contain Protected > Healthcare Information or other information of a sensitive nature. If you are > not the intended recipient, be advised that any unauthorized use, disclosure, > copying or the taking of any action in reliance on the contents of this > information is strictly prohibited. If you have received this email in error, > please immediately notify the sender via telephone or return 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] cortical surface area
Specifically, where in the aparc.stats file (or other file) is the cortical surface area? I only see default output for 'WhiteSurfArea'. Jim -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Thursday, October 12, 2017 4:16 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] cortical surface area mm2 On 10/12/2017 02:15 PM, Alexopoulos, Dimitrios wrote: > > What measure is for the cortical surface area? > > The measure in the aparc.stats file states 'WhiteSurfArea' > > Jim > > -- > -- > > The materials in this message are private and may contain Protected > Healthcare Information or other information of a sensitive nature. If > you are not the intended recipient, be advised that any unauthorized > use, disclosure, copying or the taking of any action in reliance on > the contents of this information is strictly prohibited. If you have > received this email in error, please immediately notify the sender via > telephone or return 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 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. The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] cortical surface area
mm2 On 10/12/2017 02:15 PM, Alexopoulos, Dimitrios wrote: > > What measure is for the cortical surface area? > > The measure in the aparc.stats file states ‘WhiteSurfArea’ > > Jim > > > > The materials in this message are private and may contain Protected > Healthcare Information or other information of a sensitive nature. If > you are not the intended recipient, be advised that any unauthorized > use, disclosure, copying or the taking of any action in reliance on > the contents of this information is strictly prohibited. If you have > received this email in error, please immediately notify the sender via > telephone or return 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 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] cortical surface area measurement and vertex-wise analysis
Hi Emma, Please, see below: On 13 October 2014 20:11, Emma Thompson vonecono...@gmail.com wrote: Hi Anderson, Thank you for your paper. I guess I am confused. I have analyzed my structural data with qdec, specifically looking at a measure of cortical thickness and volume. I'm considering looking at surface area as well but was told it wasn't a very good measure using qdec, I have no other information really. Could you speak to whether or not this measure is valid in so far as one runs it using qdec? The data that is used in qdec comes from mris_preproc, which uses vertexwise interpolation with Jacobian correction for local stretches/shrinkages. The amount of area is preserved globally, which is desirable, although locally it's something difficult to achieve. If without any smoothing, the spatial correlation between mris_preproc and the method in the paper is about 0.65, and the correlation at a given vertex, across subjects, varies spatially. Note, however, that the smoothing -- that is applied by default -- should increase the correlation vastly, but I don't have the exact numbers at hand to provide yet. For area, as well as for volume, the method shown in the paper is really the gold standard: it's pycnophylactic and thus guarantees that the amount of area is preserved locally everywhere in the brain during the interpolation. It's the same method used in GIS applications for geoprocessing. The downside is that the current implementation, using Matlab, is too slow (for the ico7, it can well take 10-15h per hemisphere in a single CPU). Also, in your opinion, would it be redundant to look at surface area in addition to measures of cortical thickness and cortical volume? Actually, the redundant bit here is volume. Area and thickness are uncorrelated phenotypically and genetically, and each provide different pieces of information (this is shown here http://dx.doi.org/10.1093/cercor/bhp026 and here http://www.sciencedirect.com/science/article/pii/S1053811909013160). Volume is a mixture of both, in proportions that vary across the cortical mantle. I would not consider using volume given that thickness and area are available. Moreover, volume is also an areal quantity in the sense that it requires the same methods for interpolation as surface area itself, so all that is said above about area applies also to cortical volumes. Hope this helps! All the best, Anderson On Sun, Oct 12, 2014 at 3:00 PM, Anderson M. Winkler wink...@fmrib.ox.ac.uk wrote: Hi Donna, In that same paper we also comment on the differences between expansion/contraction and absolute areal measurements assessed at each face of the surface (i.e., facewise), which can, after interpolation, be converted to vertexwise to facilitate analysis using current tools (e.g., mri_glmfit or qdec), without loss of areal quantities. All the best, Anderson On 11 October 2014 04:05, Donna Dierker do...@brainvis.wustl.edu wrote: Hi Emma, I might not be the only one who is unsure what you mean by a vertex-wise cortical surface area measure. Do you mean something like what is illustrated in figures 2 and 3 here: http://www.pnas.org/content/107/29/13135.figures-only ... which is similar, but not identical to the local gyrification index? If so, would you use this measure on surfaces before or after registration to a target atlas? Donna On Oct 10, 2014, at 4:19 PM, Emma Thompson vonecono...@gmail.com wrote: Dear Freesurfers, I recently heard that there are several disadvantages to using a measure of cortical surface area in Freesurfer, specifically due to conducting a vertex-wise analysis. Can someone help me understand why a measure of surface area using this approach might be flawed? Thanks! ___ 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.
Re: [Freesurfer] cortical surface area measurement and vertex-wise analysis
If you are using --qcache, then there is nothing wrong specifically with the qdec implementation On 10/13/2014 03:11 PM, Emma Thompson wrote: Hi Anderson, Thank you for your paper. I guess I am confused. I have analyzed my structural data with qdec, specifically looking at a measure of cortical thickness and volume. I'm considering looking at surface area as well but was told it wasn't a very good measure using qdec, I have no other information really. Could you speak to whether or not this measure is valid in so far as one runs it using qdec? Also, in your opinion, would it be redundant to look at surface area in addition to measures of cortical thickness and cortical volume? Thanks for your help and apologizes for my silly questions. On Sun, Oct 12, 2014 at 3:00 PM, Anderson M. Winkler wink...@fmrib.ox.ac.uk mailto:wink...@fmrib.ox.ac.uk wrote: Hi Donna, In that same paper we also comment on the differences between expansion/contraction and absolute areal measurements assessed at each face of the surface (i.e., facewise), which can, after interpolation, be converted to vertexwise to facilitate analysis using current tools (e.g., mri_glmfit or qdec), without loss of areal quantities. All the best, Anderson On 11 October 2014 04:05, Donna Dierker do...@brainvis.wustl.edu mailto:do...@brainvis.wustl.edu wrote: Hi Emma, I might not be the only one who is unsure what you mean by a vertex-wise cortical surface area measure. Do you mean something like what is illustrated in figures 2 and 3 here: http://www.pnas.org/content/107/29/13135.figures-only … which is similar, but not identical to the local gyrification index? If so, would you use this measure on surfaces before or after registration to a target atlas? Donna On Oct 10, 2014, at 4:19 PM, Emma Thompson vonecono...@gmail.com mailto:vonecono...@gmail.com wrote: Dear Freesurfers, I recently heard that there are several disadvantages to using a measure of cortical surface area in Freesurfer, specifically due to conducting a vertex-wise analysis. Can someone help me understand why a measure of surface area using this approach might be flawed? Thanks! ___ 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 . 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 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] cortical surface area measurement and vertex-wise analysis
Hi Anderson, Thank you for your paper. I guess I am confused. I have analyzed my structural data with qdec, specifically looking at a measure of cortical thickness and volume. I'm considering looking at surface area as well but was told it wasn't a very good measure using qdec, I have no other information really. Could you speak to whether or not this measure is valid in so far as one runs it using qdec? Also, in your opinion, would it be redundant to look at surface area in addition to measures of cortical thickness and cortical volume? Thanks for your help and apologizes for my silly questions. On Sun, Oct 12, 2014 at 3:00 PM, Anderson M. Winkler wink...@fmrib.ox.ac.uk wrote: Hi Donna, In that same paper we also comment on the differences between expansion/contraction and absolute areal measurements assessed at each face of the surface (i.e., facewise), which can, after interpolation, be converted to vertexwise to facilitate analysis using current tools (e.g., mri_glmfit or qdec), without loss of areal quantities. All the best, Anderson On 11 October 2014 04:05, Donna Dierker do...@brainvis.wustl.edu wrote: Hi Emma, I might not be the only one who is unsure what you mean by a vertex-wise cortical surface area measure. Do you mean something like what is illustrated in figures 2 and 3 here: http://www.pnas.org/content/107/29/13135.figures-only … which is similar, but not identical to the local gyrification index? If so, would you use this measure on surfaces before or after registration to a target atlas? Donna On Oct 10, 2014, at 4:19 PM, Emma Thompson vonecono...@gmail.com wrote: Dear Freesurfers, I recently heard that there are several disadvantages to using a measure of cortical surface area in Freesurfer, specifically due to conducting a vertex-wise analysis. Can someone help me understand why a measure of surface area using this approach might be flawed? Thanks! ___ 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. ___ 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] cortical surface area measurement and vertex-wise analysis
Hi Emma, Could you clarify what would be the disadvantages that you've heard about? I ask because we've studied and tried to clarify many aspects of the analysis of surface area in this paper http://www.sciencedirect.com/science/article/pii/S1053811912002996. Maybe if there's something not covered there we could try to comment then. Thanks! All the best, Anderson On 10 October 2014 22:19, Emma Thompson vonecono...@gmail.com wrote: Dear Freesurfers, I recently heard that there are several disadvantages to using a measure of cortical surface area in Freesurfer, specifically due to conducting a vertex-wise analysis. Can someone help me understand why a measure of surface area using this approach might be flawed? Thanks! ___ 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.
Re: [Freesurfer] cortical surface area measurement and vertex-wise analysis
Hi Donna, In that same paper we also comment on the differences between expansion/contraction and absolute areal measurements assessed at each face of the surface (i.e., facewise), which can, after interpolation, be converted to vertexwise to facilitate analysis using current tools (e.g., mri_glmfit or qdec), without loss of areal quantities. All the best, Anderson On 11 October 2014 04:05, Donna Dierker do...@brainvis.wustl.edu wrote: Hi Emma, I might not be the only one who is unsure what you mean by a vertex-wise cortical surface area measure. Do you mean something like what is illustrated in figures 2 and 3 here: http://www.pnas.org/content/107/29/13135.figures-only ... which is similar, but not identical to the local gyrification index? If so, would you use this measure on surfaces before or after registration to a target atlas? Donna On Oct 10, 2014, at 4:19 PM, Emma Thompson vonecono...@gmail.com wrote: Dear Freesurfers, I recently heard that there are several disadvantages to using a measure of cortical surface area in Freesurfer, specifically due to conducting a vertex-wise analysis. Can someone help me understand why a measure of surface area using this approach might be flawed? Thanks! ___ 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.
Re: [Freesurfer] cortical surface area measurement and vertex-wise analysis
Hi Emma, I might not be the only one who is unsure what you mean by a vertex-wise cortical surface area measure. Do you mean something like what is illustrated in figures 2 and 3 here: http://www.pnas.org/content/107/29/13135.figures-only … which is similar, but not identical to the local gyrification index? If so, would you use this measure on surfaces before or after registration to a target atlas? Donna On Oct 10, 2014, at 4:19 PM, Emma Thompson vonecono...@gmail.com wrote: Dear Freesurfers, I recently heard that there are several disadvantages to using a measure of cortical surface area in Freesurfer, specifically due to conducting a vertex-wise analysis. Can someone help me understand why a measure of surface area using this approach might be flawed? Thanks! ___ 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] cortical surface area related measures
Regarding Winkler et al.: http://brainder.org/2012/06/02/facewise-brain-cortical-surface-area-scripts-now-available/ On Aug 21, 2012 11:00 PM, Gregory Kirk gk...@wisc.edu wrote: Hi folks, I wanted to make sure i have everything straight w.r.t. the surface area measures. as i see there are 4 ways implemented ( somewhere ) to do cortical surface area analysis. 1. areal expansion 2. Local Gyrification Index 3. direct vertex based true surface area glm, Winkler AM et. al 4. roi based, i.e. based on the surface areas of the parcellation units in lh.aparc.a2009s.stats etc. 1. recent pub, Lisa T. Eyler et. al used the areal expansion method. was this done exactly as would be achived by using the area tab on qdec and setting up a glm ? Dale published surface area specifying some details of implementation but i was not sure if this was exactly what is implemented in qdec ? 2. LGI seems to me this is the ratio of two areas, that of the hull to the area inscribed by projecting the border of the hull onto the grey/white surface. In an e-mail Nick said LGI is a curvature based measure and that confused me a bit. gyrification is of course related to curvature but it seems the quantities actually calculated here are ratios of areas, which gives local info on surface area differences. 3. the winkler stuff is i think not publicly available yet at this time ? 4. straightforward enough not withstanding ICV corrections, etc. any words of clarification before i start trying some analysis on my group ? thank you Greg ___ 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.
Re: [Freesurfer] cortical surface area related measures
Hi Greg, I don't know what areal expansion refers to. If you want to use area (eg, the area tab in qdec), you should make sure to download the most recent version of mris_preproc (which performs a jacobian type correction) ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_preproc doug On 08/21/2012 04:59 PM, Gregory Kirk wrote: Hi folks, I wanted to make sure i have everything straight w.r.t. the surface area measures. as i see there are 4 ways implemented ( somewhere ) to do cortical surface area analysis. 1. areal expansion 2. Local Gyrification Index 3. direct vertex based true surface area glm, Winkler AM et. al 4. roi based, i.e. based on the surface areas of the parcellation units in lh.aparc.a2009s.stats etc. 1. recent pub, Lisa T. Eyler et. al used the areal expansion method. was this done exactly as would be achived by using the area tab on qdec and setting up a glm ? Dale published surface area specifying some details of implementation but i was not sure if this was exactly what is implemented in qdec ? 2. LGI seems to me this is the ratio of two areas, that of the hull to the area inscribed by projecting the border of the hull onto the grey/white surface. In an e-mail Nick said LGI is a curvature based measure and that confused me a bit. gyrification is of course related to curvature but it seems the quantities actually calculated here are ratios of areas, which gives local info on surface area differences. 3. the winkler stuff is i think not publicly available yet at this time ? 4. straightforward enough not withstanding ICV corrections, etc. any words of clarification before i start trying some analysis on my group ? thank you Greg ___ 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ 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.
