Re: [Freesurfer] wm parcellation freesurfer
That was it! (and yes, we were trying to have freesurfer do an autoparcellation for higher resolution MRI, but the full reconstruction unfortunately keeps failing on processes like skull strip). But for now, we will use the 1 mm reconstruction. Thank you for the help! Owais On Mon, Aug 3, 2015 at 12:58 PM, Bruce Fischl wrote: > Hi Owais > > are your voxels really .36mm isotropic? That is extremely high resolution > and very very rare (and hard!) if you are getting whole-brain coverage. You > can use -cm in recon-all (conform to min) to keep the resolution, but > everything will take way longer and use way more memory. I would check to > see what the true resolution of your data is first though. > > cheers > Bruce > > > > On Mon, 3 Aug 2015, Owais Syed wrote: > > Thanks for the reply, I think I misspoke though. My original T1 MRI has a >> voxel size of <0.36, 0.36, 0.36>. But when I am looking through the files >> created via recon -all (specifically wmparc.mgz, although present in other >> files as well), I noticed that the voxel size is a bit larger (about <1, >> 1, >> 1>). >> Is there a way to edit the voxel size to match the MRI during recon -all? >> >> Also how would I do that specifically for just creating wmparc.mgz from >> the >> original T1 MRI? If it is possible to do so that would be nice, otherwise >> I >> will probably try to run the entire recon -all with the new voxel size. >> >> Thanks, >> Owais >> >> On Wed, Jul 29, 2015 at 11:25 AM, Bruce Fischl < >> fis...@nmr.mgh.harvard.edu> >> wrote: >> Hi Owais >> >> do you mean the wmparc.mgz or the aparc+aseg.mgz? You can use >> mris_divide_parcellation or mris_make_face_parcellation to >> subdivide or >> make an isotropic finer scale one if you want. I believe that >> you can then >> create a new aparc+aseg from one of those and then the wmparc >> from that to >> get a finer one >> cheers >> Bruce >> >> >> On Tue, 28 Jul 2015, >> Owais Syed wrote: >> >> > Hi, >> > Is it possible to increase the number of parcellations when >> making the aparc+aseg >> > file? I have a high resolution MRI, and one parcellation will >> match every three >> > slides, but I want a better match overall. >> > >> > Thanks, >> > >> > Owais >> > >> > >> ___ >> 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. >> >> >> >> >> -- >> Owais Syed >> Chemistry, Psychology >> Rice University Class of 2016 >> >> > ___ > 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. > > -- Owais Syed Chemistry, Psychology Rice University Class of 2016 ___ 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] wm parcellation freesurfer
Hi Owais are your voxels really .36mm isotropic? That is extremely high resolution and very very rare (and hard!) if you are getting whole-brain coverage. You can use -cm in recon-all (conform to min) to keep the resolution, but everything will take way longer and use way more memory. I would check to see what the true resolution of your data is first though. cheers Bruce On Mon, 3 Aug 2015, Owais Syed wrote: Thanks for the reply, I think I misspoke though. My original T1 MRI has a voxel size of <0.36, 0.36, 0.36>. But when I am looking through the files created via recon -all (specifically wmparc.mgz, although present in other files as well), I noticed that the voxel size is a bit larger (about <1, 1, 1>). Is there a way to edit the voxel size to match the MRI during recon -all? Also how would I do that specifically for just creating wmparc.mgz from the original T1 MRI? If it is possible to do so that would be nice, otherwise I will probably try to run the entire recon -all with the new voxel size. Thanks, Owais On Wed, Jul 29, 2015 at 11:25 AM, Bruce Fischl wrote: Hi Owais do you mean the wmparc.mgz or the aparc+aseg.mgz? You can use mris_divide_parcellation or mris_make_face_parcellation to subdivide or make an isotropic finer scale one if you want. I believe that you can then create a new aparc+aseg from one of those and then the wmparc from that to get a finer one cheers Bruce On Tue, 28 Jul 2015, Owais Syed wrote: > Hi, > Is it possible to increase the number of parcellations when making the aparc+aseg > file? I have a high resolution MRI, and one parcellation will match every three > slides, but I want a better match overall. > > Thanks, > > Owais > > ___ 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. -- Owais Syed Chemistry, Psychology Rice University Class of 2016 ___ 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] wm parcellation freesurfer
Thanks for the reply, I think I misspoke though. My original T1 MRI has a voxel size of <0.36, 0.36, 0.36>. But when I am looking through the files created via recon -all (specifically wmparc.mgz, although present in other files as well), I noticed that the voxel size is a bit larger (about <1, 1, 1>). Is there a way to edit the voxel size to match the MRI during recon -all? Also how would I do that specifically for just creating wmparc.mgz from the original T1 MRI? If it is possible to do so that would be nice, otherwise I will probably try to run the entire recon -all with the new voxel size. Thanks, Owais On Wed, Jul 29, 2015 at 11:25 AM, Bruce Fischl wrote: > Hi Owais > > do you mean the wmparc.mgz or the aparc+aseg.mgz? You can use > mris_divide_parcellation or mris_make_face_parcellation to subdivide or > make an isotropic finer scale one if you want. I believe that you can then > create a new aparc+aseg from one of those and then the wmparc from that to > get a finer one > cheers > Bruce > > > On Tue, 28 Jul 2015, > Owais Syed wrote: > > > Hi, > > Is it possible to increase the number of parcellations when making the > aparc+aseg > > file? I have a high resolution MRI, and one parcellation will match > every three > > slides, but I want a better match overall. > > > > Thanks, > > > > Owais > > > > > ___ > 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. > > -- Owais Syed Chemistry, Psychology Rice University Class of 2016 ___ 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] wm parcellation freesurfer
Hi Owais do you mean the wmparc.mgz or the aparc+aseg.mgz? You can use mris_divide_parcellation or mris_make_face_parcellation to subdivide or make an isotropic finer scale one if you want. I believe that you can then create a new aparc+aseg from one of those and then the wmparc from that to get a finer one cheers Bruce On Tue, 28 Jul 2015, Owais Syed wrote: > Hi, > Is it possible to increase the number of parcellations when making the > aparc+aseg > file? I have a high resolution MRI, and one parcellation will match every > three > slides, but I want a better match overall. > > Thanks, > > Owais > > ___ 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] wm parcellation freesurfer
Hi, Is it possible to increase the number of parcellations when making the aparc+aseg file? I have a high resolution MRI, and one parcellation will match every three slides, but I want a better match overall. Thanks, Owais ___ 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.
