Hi Michael and Matt, Thanks for getting back to me, that's cleared things up a lot. I essentially wanted to know if the FreeSurfer output is expected to be different if run again and whether the surfaces in '$subject/T1w/Native/' are the same as those that would be in '$subject/T1w/$subject/surf/' if provided.
Best wishes Tara On Thu, Jun 4, 2015 at 8:29 PM, Glasser, Matthew <[email protected]> wrote: > And you cannot have rerun FreeSurfer and then expect the counts to match > what is in the HCP releases. > > Peace, > > Matt. > > From: <Harms>, Michael <[email protected]> > Date: Thursday, June 4, 2015 at 8:39 AM > To: Tara Ganepola <[email protected]>, "[email protected]" < > [email protected]> > Subject: Re: [HCP-Users] Freesurfer pipeline and subject's native surfaces > > Hi, > Are you comparing the FS output in > '$subject/T1w/$subject/surf/{lh,rh}.white' to > '$subject/T1w/Native/$subject.{L,R}.white.native.surf.gii? > Because those should indeed have the same number of vertices and faces for > a given hemisphere. > > Rather than using 'mris_convert', what happens if you just use > 'mris_info' directly on the lh.white file, and 'wb_command > -file-information' on the L.white.native.surf.gii file? > > cheers, > -MH > > -- > Michael Harms, Ph.D. > ----------------------------------------------------------- > Conte Center for the Neuroscience of Mental Disorders > Washington University School of Medicine > Department of Psychiatry, Box 8134 > 660 South Euclid Ave. Tel: 314-747-6173 > St. Louis, MO 63110 Email: [email protected] > > From: Tara Ganepola <[email protected]> > Date: Thursday, June 4, 2015 11:07 AM > To: "[email protected]" <[email protected]> > Subject: [HCP-Users] Freesurfer pipeline and subject's native surfaces > > Hello, > > My question is related to the FreeSurfer pipeline scripts and the > contents of the 'subject/T1w/Native/' directories. After running the > FreeSurferPipelineBatch.sh locally should I expect the surfaces to be > identical to those found in 'subject/T1w/Native/' or is there an additional > step of processing between these? > > I have done this for a few subjects and noticed that the vertex count is > different. For example for subject 100307 the file > 100307.R.white.native.surf.gii has 128346 vertices and the output of the > FreeSurfer pipeline, rh.white has 128900. (the vertex counts were > determined by converting to ascii format using mris_convert). > > Ultimately, I am aiming to sample the diffusion weighted data at > different cortical depths with an in house script that required > freesurfer's binary surface format. I would like the best possible surfaces > for subjects in their native space, the quickest method would be to convert > the provided gifti files back, but as the files seem to have different > vertex counts I was unsure whether they are equivalent or if they have been > through some transformation? > > Many thanks > Tara > > _______________________________________________ > HCP-Users mailing list > [email protected] > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > > ------------------------------ > > 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. > > _______________________________________________ > HCP-Users mailing list > [email protected] > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > > ------------------------------ > > 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. > On Thu, Jun 4, 2015 at 8:29 PM, Glasser, Matthew <[email protected]> wrote: > And you cannot have rerun FreeSurfer and then expect the counts to match > what is in the HCP releases. > > Peace, > > Matt. > > From: <Harms>, Michael <[email protected]> > Date: Thursday, June 4, 2015 at 8:39 AM > To: Tara Ganepola <[email protected]>, "[email protected]" < > [email protected]> > Subject: Re: [HCP-Users] Freesurfer pipeline and subject's native surfaces > > Hi, > Are you comparing the FS output in > '$subject/T1w/$subject/surf/{lh,rh}.white' to > '$subject/T1w/Native/$subject.{L,R}.white.native.surf.gii? > Because those should indeed have the same number of vertices and faces for > a given hemisphere. > > Rather than using 'mris_convert', what happens if you just use > 'mris_info' directly on the lh.white file, and 'wb_command > -file-information' on the L.white.native.surf.gii file? > > cheers, > -MH > > -- > Michael Harms, Ph.D. > ----------------------------------------------------------- > Conte Center for the Neuroscience of Mental Disorders > Washington University School of Medicine > Department of Psychiatry, Box 8134 > 660 South Euclid Ave. Tel: 314-747-6173 > St. Louis, MO 63110 Email: [email protected] > > From: Tara Ganepola <[email protected]> > Date: Thursday, June 4, 2015 11:07 AM > To: "[email protected]" <[email protected]> > Subject: [HCP-Users] Freesurfer pipeline and subject's native surfaces > > Hello, > > My question is related to the FreeSurfer pipeline scripts and the > contents of the 'subject/T1w/Native/' directories. After running the > FreeSurferPipelineBatch.sh locally should I expect the surfaces to be > identical to those found in 'subject/T1w/Native/' or is there an additional > step of processing between these? > > I have done this for a few subjects and noticed that the vertex count is > different. For example for subject 100307 the file > 100307.R.white.native.surf.gii has 128346 vertices and the output of the > FreeSurfer pipeline, rh.white has 128900. (the vertex counts were > determined by converting to ascii format using mris_convert). > > Ultimately, I am aiming to sample the diffusion weighted data at > different cortical depths with an in house script that required > freesurfer's binary surface format. I would like the best possible surfaces > for subjects in their native space, the quickest method would be to convert > the provided gifti files back, but as the files seem to have different > vertex counts I was unsure whether they are equivalent or if they have been > through some transformation? > > Many thanks > Tara > > _______________________________________________ > HCP-Users mailing list > [email protected] > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > > ------------------------------ > > 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. > > _______________________________________________ > HCP-Users mailing list > [email protected] > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > > ------------------------------ > > 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. > _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
